diff --git a/cases/1-one-compartment/meta/src/shared-constants.heta.json b/cases/1-one-compartment/meta/src/shared-constants.heta.json deleted file mode 100644 index 98879603..00000000 --- a/cases/1-one-compartment/meta/src/shared-constants.heta.json +++ /dev/null @@ -1,231 +0,0 @@ -[ - { - "class": "Const", - "id": "kabs", - "num": 0.01, - "action": "upsert" - }, - { - "class": "Const", - "id": "kel", - "num": 0.01, - "action": "upsert" - }, - { - "class": "Const", - "id": "Vmax", - "num": 1.2, - "action": "upsert" - }, - { - "class": "Const", - "id": "Km", - "num": 1.1, - "action": "upsert" - }, - { - "action": "setNS", - "space": "one_comp" - }, - { - "space": "one_comp", - "action": "importNS", - "fromSpace": "nameless" - }, - { - "space": "one_comp", - "id": "a0", - "class": "Species", - "compartment": "comp0", - "isAmount": true, - "action": "upsert" - }, - { - "space": "one_comp", - "id": "s1", - "class": "Species", - "compartment": "comp1", - "action": "upsert" - }, - { - "space": "one_comp", - "id": "comp0", - "class": "Compartment", - "assignments": { - "start_": 1 - }, - "action": "upsert" - }, - { - "space": "one_comp", - "id": "comp1", - "class": "Compartment", - "assignments": { - "start_": 5.2 - }, - "action": "upsert" - }, - { - "space": "one_comp", - "id": "vabs", - "class": "Reaction", - "actors": "a0 -> s1", - "action": "upsert" - }, - { - "space": "one_comp", - "id": "vel", - "class": "Reaction", - "actors": "s1 ->", - "action": "upsert" - }, - { - "space": "one_comp", - "id": "vabs", - "assignments": { - "ode_": "kabs*a0" - }, - "action": "upsert" - }, - { - "space": "one_comp", - "id": "vel", - "assignments": { - "ode_": "kel*s1*comp1" - }, - "action": "upsert" - }, - { - "space": "one_comp", - "id": "a0", - "assignments": { - "start_": 10 - }, - "action": "upsert" - }, - { - "space": "one_comp", - "id": "s1", - "assignments": { - "start_": 0 - }, - "action": "upsert" - }, - { - "action": "setNS", - "space": "one_comp_saturation" - }, - { - "space": "one_comp_saturation", - "action": "importNS", - "fromSpace": "nameless" - }, - { - "space": "one_comp_saturation", - "id": "a0", - "class": "Species", - "compartment": "comp0", - "isAmount": true, - "action": "upsert" - }, - { - "space": "one_comp_saturation", - "id": "s1", - "class": "Species", - "compartment": "comp1", - "action": "upsert" - }, - { - "space": "one_comp_saturation", - "id": "comp0", - "class": "Compartment", - "assignments": { - "start_": 1 - }, - "action": "upsert" - }, - { - "space": "one_comp_saturation", - "id": "comp1", - "class": "Compartment", - "assignments": { - "start_": 5.2 - }, - "action": "upsert" - }, - { - "space": "one_comp_saturation", - "id": "vabs", - "class": "Reaction", - "actors": "a0 -> s1", - "action": "upsert" - }, - { - "space": "one_comp_saturation", - "id": "vel", - "class": "Reaction", - "actors": "s1 ->", - "action": "upsert" - }, - { - "space": "one_comp_saturation", - "id": "vabs", - "assignments": { - "ode_": "kabs*a0" - }, - "action": "upsert" - }, - { - "space": "one_comp_saturation", - "id": "vel", - "assignments": { - "ode_": "Vmax*s1*comp1/(Km + s1)" - }, - "action": "upsert" - }, - { - "space": "one_comp_saturation", - "id": "a0", - "assignments": { - "start_": 10 - }, - "action": "upsert" - }, - { - "space": "one_comp_saturation", - "id": "s1", - "assignments": { - "start_": 0 - }, - "action": "upsert" - }, - { - "action": "export", - "format": "JSON", - "filepath": "json" - }, - { - "action": "export", - "format": "SLV", - "spaceFilter": "one_comp", - "filepath": "slv_non_saturable" - }, - { - "action": "export", - "format": "SLV", - "spaceFilter": "one_comp_saturation", - "filepath": "slv_saturable" - }, - { - "action": "export", - "format": "Mrgsolve", - "spaceFilter": "one_comp", - "filepath": "non_saturable" - }, - { - "action": "export", - "format": "Mrgsolve", - "spaceFilter": "one_comp_saturation", - "filepath": "mrg_saturable" - } -] \ No newline at end of file diff --git a/cases/1-one-compartment/platform.yml b/cases/1-one-compartment/platform.yml index 2dc329c3..82634072 100644 --- a/cases/1-one-compartment/platform.yml +++ b/cases/1-one-compartment/platform.yml @@ -2,8 +2,24 @@ id: mm builderVersion: '*' options: logLevel: info - debug: true + debug: false unitsCheck: false importModule: type: heta source: src/shared-constants.heta +export: + - format: JSON + filepath: json + - format: SLV + filepath: slv + spaceFilter: one_comp + - format: SLV + filepath: slv_saturable + spaceFilter: one_comp_saturation + - format: Mrgsolve + filepath: non_saturable + spaceFilter: one_comp + - format: Mrgsolve + filepath: mrg_saturable + spaceFilter: one_comp_saturation + diff --git a/cases/1-one-compartment/src/dividing.heta b/cases/1-one-compartment/src/dividing.heta index c0ff1560..bdfce6fc 100644 --- a/cases/1-one-compartment/src/dividing.heta +++ b/cases/1-one-compartment/src/dividing.heta @@ -7,10 +7,3 @@ end include non-saturable.heta; include saturable.heta; - -//#export {space: one_comp, format: SBML, filepath: sbml_non_saturable}; -//#export {space: one_comp_saturation, format: SBML, filepath: sbml_saturable}; -#export { filepath: json, format: JSON }; -#export { filepath: slv_non_saturable, spaceFilter: one_comp, format: SLV }; -#export { filepath: slv_saturable, spaceFilter: one_comp_saturation, format: SLV }; - diff --git a/cases/1-one-compartment/src/shared-constants.heta b/cases/1-one-compartment/src/shared-constants.heta index 3f5c968d..808b32b2 100644 --- a/cases/1-one-compartment/src/shared-constants.heta +++ b/cases/1-one-compartment/src/shared-constants.heta @@ -36,11 +36,3 @@ namespace one_comp_saturation begin a0 []= 10; // initial value s1 []= 0; end - -//#export {space: one_comp, filepath: sbml_non_saturable, format: SBML}; -//#export {space: one_comp_saturation, filepath: sbml_saturable, format: SBML}; -#export {format: JSON, filepath: json}; -#export {format: SLV, spaceFilter: one_comp, filepath: slv_non_saturable}; -#export {format: SLV, spaceFilter: one_comp_saturation, filepath: slv_saturable}; -#export {format: Mrgsolve, spaceFilter: one_comp, filepath: non_saturable}; -#export {format: Mrgsolve, spaceFilter: one_comp_saturation, filepath: mrg_saturable}; diff --git a/cases/1-one-compartment/src/single-model.heta b/cases/1-one-compartment/src/single-model.heta index 475daf56..68d1c4c2 100644 --- a/cases/1-one-compartment/src/single-model.heta +++ b/cases/1-one-compartment/src/single-model.heta @@ -20,8 +20,3 @@ namespace one_comp begin a0 []= 10; // initial value s1 []= 0; end - -//#export {space: one_comp, filepath: sbml, format: SBML}; -#export {spaceFilter: one_comp, filepath: json, format: JSON}; -#export {spaceFilter: one_comp, filepath: slv, format: SLV}; - diff --git a/cases/2-cells/meta/src/index.heta#0.json b/cases/2-cells/meta/src/index.heta#0.json new file mode 100644 index 00000000..cfa173b9 --- /dev/null +++ b/cases/2-cells/meta/src/index.heta#0.json @@ -0,0 +1,272 @@ +[ + { + "action": "upsert", + "class": "Const", + "id": "plasma", + "num": 2.5 + }, + { + "action": "upsert", + "class": "Const", + "id": "k_prol", + "num": 0.0001 + }, + { + "action": "upsert", + "class": "Const", + "id": "AXP_neu", + "num": 0.1 + }, + { + "action": "setNS", + "space": "invitro" + }, + { + "action": "import", + "space": "invitro", + "id": "AXP_neu", + "fromId": "AXP_neu", + "fromSpace": "nameless" + }, + { + "action": "include", + "space": "invitro", + "source": "Y:\\heta-compiler\\cases\\2-cells\\src\\neu.heta" + }, + { + "action": "upsert", + "space": "invitro" + }, + { + "action": "upsert", + "space": "invitro" + }, + { + "action": "upsert", + "space": "invitro" + }, + { + "action": "upsert", + "space": "invitro", + "id": "tot_vol", + "class": "Compartment", + "assignments": { + "start_": 0.1 + } + }, + { + "action": "upsert", + "space": "invitro", + "id": "P1_mean", + "class": "Record", + "assignments": { + "ode_": "( P1_ext * ext + P1_neu * neu_vol ) / tot_vol" + } + }, + { + "action": "upsert", + "space": "invitro", + "id": "ext", + "assignments": { + "start_": 1 + } + }, + { + "action": "upsert", + "space": "invitro", + "id": "S1", + "assignments": { + "start_": 150 + } + }, + { + "action": "upsert", + "space": "invitro", + "id": "IL15_ext", + "assignments": { + "start_": 0 + } + }, + { + "action": "upsert", + "space": "invitro", + "id": "neu_count", + "assignments": { + "start_": 1000000 + } + }, + { + "action": "upsert", + "space": "invitro", + "id": "P1_ext", + "assignments": { + "start_": 0 + } + }, + { + "action": "upsert", + "space": "invitro", + "id": "P1_neu", + "assignments": { + "start_": 0 + } + }, + { + "action": "upsert", + "space": "invitro", + "id": "ATP_neu", + "assignments": { + "start_": "AXP_neu * K_eq_ADP / (1 + K_eq_ADP)" + } + }, + { + "action": "upsert", + "space": "invitro", + "id": "ADP_neu", + "assignments": { + "start_": "AXP_neu / (1 + K_eq_ADP)" + } + }, + { + "action": "setNS", + "space": "invivo" + }, + { + "action": "import", + "space": "invivo", + "id": "plasma", + "fromId": "plasma", + "fromSpace": "nameless" + }, + { + "action": "import", + "space": "invivo", + "id": "k_prol", + "fromId": "k_prol", + "fromSpace": "nameless" + }, + { + "action": "include", + "space": "invivo", + "source": "Y:\\heta-compiler\\cases\\2-cells\\src\\neu.heta" + }, + { + "action": "upsert", + "space": "invivo" + }, + { + "action": "upsert", + "space": "invivo", + "id": "blood", + "class": "Compartment", + "assignments": { + "start_": 5.2 + } + }, + { + "action": "upsert", + "space": "invivo", + "id": "neu_count", + "class": "Species", + "compartment": "blood" + }, + { + "action": "update", + "space": "invivo", + "id": "S1", + "compartment": "blood" + }, + { + "action": "delete", + "space": "invivo", + "id": "tot_vol" + }, + { + "action": "upsert", + "space": "invivo", + "id": "ext", + "assignments": { + "ode_": "plasma" + } + }, + { + "action": "upsert", + "space": "invivo", + "id": "AXP_neu", + "class": "Record", + "assignments": { + "start_": 0.1 + } + }, + { + "action": "upsert", + "space": "invivo", + "id": "IL15_ext", + "assignments": { + "start_": 0 + } + }, + { + "action": "upsert", + "space": "invivo", + "id": "neu_count", + "assignments": { + "start_": 1e-9 + } + }, + { + "action": "upsert", + "space": "invivo", + "id": "r_prol_neu", + "class": "Reaction", + "actors": "-> neu_count" + }, + { + "action": "upsert", + "space": "invivo", + "id": "r_prol_neu", + "assignments": { + "ode_": "k_prol * neu_count" + } + }, + { + "action": "upsert", + "space": "invivo", + "id": "S1", + "assignments": { + "start_": 10 + } + }, + { + "action": "upsert", + "space": "invivo", + "id": "P1_ext", + "assignments": { + "start_": 0 + } + }, + { + "action": "upsert", + "space": "invivo", + "id": "P1_neu", + "assignments": { + "start_": 0 + } + }, + { + "action": "upsert", + "space": "invivo", + "id": "ATP_neu", + "assignments": { + "start_": "AXP_neu * K_eq_ADP / (1 + K_eq_ADP)" + } + }, + { + "action": "upsert", + "space": "invivo", + "id": "ADP_neu", + "assignments": { + "start_": "AXP_neu / (1 + K_eq_ADP)" + } + } +] \ No newline at end of file diff --git a/cases/2-cells/meta/src/neu.heta#0.json b/cases/2-cells/meta/src/neu.heta#0.json new file mode 100644 index 00000000..82c8cfdb --- /dev/null +++ b/cases/2-cells/meta/src/neu.heta#0.json @@ -0,0 +1,180 @@ +[ + { + "action": "upsert", + "class": "Const", + "id": "neu_size", + "num": 1e-12 + }, + { + "action": "upsert", + "class": "Const", + "id": "K_eq_ADP", + "num": 10 + }, + { + "action": "upsert", + "class": "Const", + "id": "ksyn_ATP", + "num": 0.0001 + }, + { + "action": "upsert", + "class": "Const", + "id": "ksyn_P1", + "num": 0.01 + }, + { + "action": "upsert", + "class": "Const", + "id": "Km_S1", + "num": 1.2 + }, + { + "action": "upsert", + "class": "Const", + "id": "k_tr_P1", + "num": 0.013 + }, + { + "action": "upsert", + "class": "Const", + "id": "ATP_neu", + "num": 10000 + }, + { + "action": "setNS", + "space": "abstract_neu" + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "tot_vol", + "class": "Compartment" + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "S1", + "class": "Species", + "compartment": "tot_vol" + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "neu_count", + "class": "Species", + "compartment": "tot_vol", + "isAmount": true + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "neu_vol", + "class": "Compartment" + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "neu_vol", + "assignments": { + "ode_": "neu_count * neu_size" + } + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "ATP_neu", + "class": "Species", + "compartment": "neu_vol" + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "ADP_neu", + "class": "Species", + "compartment": "neu_vol" + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "P1_neu", + "class": "Species", + "compartment": "neu_vol" + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "ext", + "class": "Compartment" + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "ext", + "assignments": { + "ode_": "tot_vol - neu_vol" + } + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "P1_ext", + "class": "Species", + "compartment": "ext" + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "IL15_ext", + "class": "Species", + "compartment": "ext" + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "r_syn_ATP", + "class": "Reaction", + "actors": "ADP_neu -> ATP_neu" + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "r_syn_ATP", + "assignments": { + "ode_": "ksyn_ATP * neu_vol * (ADP_neu - ATP_neu/K_eq_ADP)" + } + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "r_syn_P1", + "class": "Reaction", + "actors": "2ATP_neu + S1 -> 2ADP_neu + P1_neu", + "modifiers": [ + "IL15_ext" + ] + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "r_syn_P1", + "assignments": { + "ode_": "ksyn_P1 * neu_vol * S1 / (S1 + Km_S1) * ATP_neu^2" + } + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "r_tr_P1", + "class": "Reaction", + "actors": "P1_neu -> P1_ext" + }, + { + "action": "upsert", + "space": "abstract_neu", + "id": "r_tr_P1", + "assignments": { + "ode_": "k_tr_P1 * neu_vol * (P1_neu - P1_ext)" + } + } +] \ No newline at end of file diff --git a/cases/2-cells/platform.yml b/cases/2-cells/platform.yml index 4aeeba14..0afd057b 100644 --- a/cases/2-cells/platform.yml +++ b/cases/2-cells/platform.yml @@ -7,3 +7,30 @@ options: importModule: type: heta source: src/index.heta +export: + - format: YAML + filepath: yaml_invitro + spaceFilter: invitro + - format: YAML + filepath: yaml_invivo + spaceFilter: invivo + - format: DBSolve + filepath: slv_invitro + spaceFilter: invitro + - format: DBSolve + filepath: slv_invivo + spaceFilter: invivo + - format: Mrgsolve + filepath: mrg_invitro + spaceFilter: invitro + - format: Mrgsolve + filepath: mrg_invivo + spaceFilter: invivo + - format: SBML + filepath: sbml_invitro + spaceFilter: invitro + - format: SBML + filepath: sbml_invivo + spaceFilter: invivo + - format: Dot + filepath: graph diff --git a/cases/2-cells/src/index.heta b/cases/2-cells/src/index.heta index e6a5b3ee..8769546d 100644 --- a/cases/2-cells/src/index.heta +++ b/cases/2-cells/src/index.heta @@ -1,7 +1,7 @@ block @Const begin plasma = 2.5; k_prol = 1e-4; - AXP_neu = 0.1; + AXP_neu = 0.1; end namespace invitro begin @@ -49,14 +49,3 @@ namespace invivo begin ATP_neu .= AXP_neu * K_eq_ADP / (1 + K_eq_ADP); ADP_neu .= AXP_neu / (1 + K_eq_ADP); end - -#export {spaceFilter: invitro, format: YAML, filepath: yaml_invitro}; -#export {spaceFilter: invivo, format: YAML, filepath: yaml_invivo}; -#export {spaceFilter: invitro, format: DBSolve, filepath: slv_invitro}; -#export {spaceFilter: invivo, format: DBSolve, filepath: slv_invivo}; -#export {spaceFilter: invitro, format: Mrgsolve, filepath: mrg_invitro}; -#export {spaceFilter: invivo, format: Mrgsolve, filepath: mrg_invivo}; -#export {spaceFilter: invitro, format: SBML, filepath: sbml_invitro}; -#export {spaceFilter: invivo, format: SBML, filepath: sbml_invivo}; -#export {format: Dot, filepath: graph}; -