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metelkin committed Jun 13, 2024
1 parent fe700ac commit 3b47b9b
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14 changes: 14 additions & 0 deletions latest/cases/00027/l3v2/heta-code/output.heta
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t @TimeScale { units: second, };

compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.534;

S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment;
S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;

reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };
reaction1 := compartment * k__reaction1_local * S1;

k__reaction1_local @Const { } = 100;

60 changes: 60 additions & 0 deletions latest/cases/00027/l3v2/json/output.json
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[
{
"id": "t",
"units": "second"
},
{
"class": "Compartment",
"id": "compartment",
"title": "compartment",
"units": "litre",
"assignments": {
"start_": "0.534"
},
"boundary": true
},
{
"class": "Species",
"id": "S1",
"title": "S1",
"units": "mole/litre",
"assignments": {
"start_": "0.015 / compartment"
},
"compartment": "compartment"
},
{
"class": "Species",
"id": "S2",
"title": "S2",
"units": "mole/litre",
"assignments": {
"start_": "0 / compartment"
},
"compartment": "compartment"
},
{
"class": "Const",
"id": "k__reaction1_local",
"num": 100
},
{
"class": "Reaction",
"id": "reaction1",
"title": "reaction1",
"assignments": {
"ode_": "compartment * k__reaction1_local * S1"
},
"actors": [
{
"target": "S2",
"stoichiometry": 1
},
{
"target": "S1",
"stoichiometry": -1
}
],
"reversible": false
}
]
13 changes: 4 additions & 9 deletions latest/cases/00027/output.heta
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Expand Up @@ -42,18 +42,13 @@ where they appear in expressions.
*/


volume #defineUnit { units: litre, };
area #defineUnit { units: metre^2, };
length #defineUnit { units: metre, };
substance #defineUnit { units: mole, };
time #defineUnit { units: second, };

t @TimeScale { };
t @TimeScale { units: second, };

compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 0.534;
compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 0.534;

S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 0.015 / compartment;
S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment;
S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 0.015 / compartment;
S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;

reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };
reaction1 := compartment * k__reaction1_local * S1;
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18 changes: 18 additions & 0 deletions latest/cases/00057/l3v2/heta-code/output.heta
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t @TimeScale { units: second, };

compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;

S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 3e-4 / compartment;
S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;
S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment;

reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };
reaction1 := compartment * k__reaction1_local * S1;
reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };
reaction2 := compartment * k__reaction2_local * S2;

k__reaction1_local @Const { } = 1;
k__reaction2_local @Const { } = 2;

94 changes: 94 additions & 0 deletions latest/cases/00057/l3v2/json/output.json
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[
{
"id": "t",
"units": "second"
},
{
"class": "Compartment",
"id": "compartment",
"title": "compartment",
"units": "litre",
"assignments": {
"start_": "1"
},
"boundary": true
},
{
"class": "Species",
"id": "S1",
"title": "S1",
"units": "mole/litre",
"assignments": {
"start_": "3e-4 / compartment"
},
"compartment": "compartment"
},
{
"class": "Species",
"id": "S2",
"title": "S2",
"units": "mole/litre",
"assignments": {
"start_": "0 / compartment"
},
"compartment": "compartment"
},
{
"class": "Species",
"id": "S3",
"title": "S3",
"units": "mole/litre",
"assignments": {
"start_": "0 / compartment"
},
"compartment": "compartment"
},
{
"class": "Const",
"id": "k__reaction1_local",
"num": 1
},
{
"class": "Reaction",
"id": "reaction1",
"title": "reaction1",
"assignments": {
"ode_": "compartment * k__reaction1_local * S1"
},
"actors": [
{
"target": "S2",
"stoichiometry": 1
},
{
"target": "S1",
"stoichiometry": -1
}
],
"reversible": false
},
{
"class": "Const",
"id": "k__reaction2_local",
"num": 2
},
{
"class": "Reaction",
"id": "reaction2",
"title": "reaction2",
"assignments": {
"ode_": "compartment * k__reaction2_local * S2"
},
"actors": [
{
"target": "S3",
"stoichiometry": 1
},
{
"target": "S2",
"stoichiometry": -1
}
],
"reversible": false
}
]
15 changes: 5 additions & 10 deletions latest/cases/00057/output.heta
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Expand Up @@ -37,19 +37,14 @@ where they appear in expressions.
*/


volume #defineUnit { units: litre, };
area #defineUnit { units: metre^2, };
length #defineUnit { units: metre, };
substance #defineUnit { units: mole, };
time #defineUnit { units: second, };

t @TimeScale { };
t @TimeScale { units: second, };

compartment @Compartment 'compartment' { units: volume, boundary: true, } .= 1;
compartment @Compartment 'compartment' { units: litre, boundary: true, } .= 1;

S1 @Species 'S1' { units: substance/volume, compartment: compartment, } .= 3e-4 / compartment;
S2 @Species 'S2' { units: substance/volume, compartment: compartment, } .= 0 / compartment;
S3 @Species 'S3' { units: substance/volume, compartment: compartment, } .= 0 / compartment;
S1 @Species 'S1' { units: mole/litre, compartment: compartment, } .= 3e-4 / compartment;
S2 @Species 'S2' { units: mole/litre, compartment: compartment, } .= 0 / compartment;
S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compartment;

reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };
reaction1 := compartment * k__reaction1_local * S1;
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3 changes: 2 additions & 1 deletion latest/cases/00058/l3v2/heta-code/output.heta
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Expand Up @@ -11,7 +11,8 @@ S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compart
reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };
reaction1 := compartment * k * S1;
reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };
reaction2 := compartment * k * S2;
reaction2 := compartment * k__reaction2_local * S2;

k__reaction2_local @Const { } = 2;
k @Const 'k' { } = 1;

7 changes: 6 additions & 1 deletion latest/cases/00058/l3v2/json/output.json
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Expand Up @@ -62,12 +62,17 @@
],
"reversible": false
},
{
"class": "Const",
"id": "k__reaction2_local",
"num": 2
},
{
"class": "Reaction",
"id": "reaction2",
"title": "reaction2",
"assignments": {
"ode_": "compartment * k * S2"
"ode_": "compartment * k__reaction2_local * S2"
},
"actors": [
{
Expand Down
3 changes: 2 additions & 1 deletion latest/cases/00058/output.heta
Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,8 @@ S3 @Species 'S3' { units: mole/litre, compartment: compartment, } .= 0 / compart
reaction1 @Reaction 'reaction1' { actors: S1 = S2, reversible: false, };
reaction1 := compartment * k * S1;
reaction2 @Reaction 'reaction2' { actors: S2 = S3, reversible: false, };
reaction2 := compartment * k * S2;
reaction2 := compartment * k__reaction2_local * S2;

k__reaction2_local @Const { } = 2;
k @Const 'k' { } = 1;

25 changes: 25 additions & 0 deletions latest/cases/00101/l2v5/heta-code/output.heta
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volume #defineUnit { units: litre, };
area #defineUnit { units: metre^2, };
length #defineUnit { units: metre, };
substance #defineUnit { units: mole, };
time #defineUnit { units: second, };
multiply #defineFunction { arguments: [x, y], math: x * y, };

t @TimeScale { };

compartment @Compartment 'compartment' { units: area, boundary: true, } .= 1;

S1 @Species 'S1' { units: substance/area, compartment: compartment, } .= 1e-15 / compartment;
S2 @Species 'S2' { units: substance/area, compartment: compartment, } .= 1e-4 / compartment;
S3 @Species 'S3' { units: substance/area, compartment: compartment, } .= 2e-4 / compartment;
S4 @Species 'S4' { units: substance/area, compartment: compartment, } .= 1e-4 / compartment;

reaction1 @Reaction 'reaction1' { actors: S1 + S2 = S3 + S4, reversible: false, };
reaction1 := compartment * multiply(k1, multiply(S1, S2));
reaction2 @Reaction 'reaction2' { actors: S3 + S4 = S1 + S2, reversible: false, };
reaction2 := compartment * k2 * S3 * S4;

k1 @Record 'k1' { } .= 7500;
k2 @Record 'k2' { } .= 2500;

10 changes: 10 additions & 0 deletions latest/cases/00101/l2v5/index.heta
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#defineUnit volume { units: litre };
#defineUnit area { units: metre^2 };
#defineUnit length { units: metre };
#defineUnit substance { units: mole };
#defineUnit time { units: second };

#include { source: ../model-sbml-l2v5.xml, type: sbml };

#export { format: HetaCode };
#export { format: JSON };
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