add complete word

cases/0001/index0.heta

@@ -1,5 +1,5 @@
 /*
-    Create the simplest QSP model in Heta notation.
+    Create the complete (full) simplest QSP model in Heta notation.
     Something like "hello world" in programming.
     One compartment, one species, one reaction with mass action.
 */

cases/0002/index0.heta

@@ -1,5 +1,5 @@
 /*
-  Create simple kinetic model with two species and one reaction in Heta notation.
+  Create complete simple kinetic model with two species and one reaction in Heta notation.
   Mass action kinetics is used.
 */
 // index.heta

cases/0002/index1.heta

@@ -1,5 +1,5 @@
 /*
-  Create simple Heta model with Michaelis-Menten (MM) type reaction for r1.
+  Create complete simple Heta model with Michaelis-Menten (MM) type reaction for r1.
 */
 // index.heta
 

cases/0002/index2.heta

@@ -1,5 +1,5 @@
 /*
-  Create simple Heta model with reversible Michaelis-Menten (MM) kinetics.
+  Create complete simple Heta model with reversible Michaelis-Menten (MM) kinetics.
 */
 // index.heta
 

cases/0002/index3.heta

@@ -1,5 +1,5 @@
 /*
-  Create simple model with reversible MM.
+  Create complete simple model with reversible MM.
   Add units to all components from qsp-units.heta from default template.
 */
 // index.heta

cases/0002/index4.heta

@@ -1,5 +1,5 @@
 /*
-  Create reversible MM kinetics model with 1 substrate and 1 product.
+  Create reversible MM kinetics complete model with 1 substrate and 1 product.
   Set units for all quantities without defineUnits. Units must be: second, micro moles, litre, etc.
 */
 // index.heta

cases/0002/index5.heta

@@ -1,5 +1,5 @@
 /*
-  Create simple model with reversible MM.
+  Create simple complete Heta model with reversible MM.
   Use short names for units like in qsp-units.heta
 */
 // index.heta

cases/0003/index0.heta

@@ -1,5 +1,5 @@
 /*
-    Create simple Heta model with constant synthesis of some metabolite.
+    Create complete simple Heta model with constant synthesis of some metabolite.
 */
 // index.heta
 

cases/0003/index1.heta

@@ -1,6 +1,5 @@
 /*
-    Do not use export action.
-    Create Heta model for constant production of species p1 in compartment comp1.
+    Create complete Heta model for constant production of species p1 in compartment comp1.
 */
 // index.heta
 

cases/0003/index3.heta

@@ -1,5 +1,5 @@
 /*
-    Create Heta model where product is transformed from boundary (buffered) species.
+    Create complete Heta model where product is transformed from boundary (buffered) species.
 */
 // index.heta
 

cases/0003/index4.heta

@@ -1,5 +1,5 @@
 /*
-    Build Heta model which desribes the transport of a substance from one compartment to another.
+    Build complete Heta model which desribes the transport of a substance from one compartment to another.
     The concentration of source species is constant and the transport is described by a first order reaction.
 */
 // index.heta

cases/0004/index0.heta

@@ -1,5 +1,5 @@
 /*
-    Create Heta model with one substrate and zero product with mass-action law.
+    Create complete Heta model with one substrate and zero product with mass-action law.
 */
 // index.heta
 

cases/0004/index1.heta

@@ -1,5 +1,5 @@
 /*
-    Create Heta model where substrate is eliminagted with stoichiometry 2.
+    Create complete Heta model where substrate is eliminagted with stoichiometry 2.
 */
 // index.heta
 

cases/0004/index2.heta

@@ -1,5 +1,5 @@
 /*
-    Write Heta model with reaction where substrate is transformed to product with stoichiometry 2:1.
+    Write complete Heta model with reaction where substrate is transformed to product with stoichiometry 2:1.
 */
 // index.heta
 

cases/0004/index3.heta

@@ -1,5 +1,5 @@
 /*
-    Create a Heta model with a single compartment, and reaction with stoicheometry
+    Create a complete Heta model with a single compartment, and reaction with stoicheometry
     2s1 + 3s2 => p1 + p2 
 */
 // index.heta

cases/0004/index4.heta

@@ -1,5 +1,5 @@
 /*
-    Create Heta model with reversible reaction and stoicheometry: 2s1 + 3s2 <=> p1 + p2.
+    Create complete Heta model with reversible reaction and stoicheometry: 2s1 + 3s2 <=> p1 + p2.
     Use mass action law.
 */
 // index.heta

cases/0004/index5.heta

@@ -1,5 +1,5 @@
 /*
-    Create Heta model with reversible reaction and stoicheometry: 2s1 + 3s2 <=> p1 + p2.
+    Create complete Heta model with reversible reaction and stoicheometry: 2s1 + 3s2 <=> p1 + p2.
     Use mass action law.
     Define units for time, volume, and concentration.
 */

result.jsonl

@@ -7,14 +7,11 @@
 {"prompt":" Build Heta model which desribes the transport of a substance from one compartment to another. The concentration of source species is constant and the transport is described by a first order reaction. ","completion":"// index.heta\n\n// compartments\ncomp1 @Compartment .= 1;\ncomp2 @Compartment .= 3;\n\n// species\ns1 @Species {compartment: comp1, boundary: true} .= 100;\np1 @Species {compartment: comp2} .= 0;\n\n// reactions\nr1 @Reaction {actors: s1 => p1} := k1 * s1 * comp1;\n\n// parameters\nk1 @Const = 0.1;\n"}
 {"prompt":" Create Heta model where product is transformed from boundary (buffered) species. ","completion":"// index.heta\n\n// compartments\ncomp1 @Compartment .= 1;\n\n// species\np1 @Species {compartment: comp1} .= 0;\ns1 @Species {compartment: comp1, boundary: true} .= 100;\n\n// reactions\nr1 @Reaction {actors: s1 => p1} := k1 * s1 * comp1;\n\n// parameters\nk1 @Const = 0.1;\n"}
 {"prompt":" Do not use export action. Create Heta model for constant production of species p1 in compartment comp1. ","completion":"// index.heta\n\n// compartments\ncomp1 @Compartment .= 1;\n\n// species\np1 @Species {compartment: comp1} .= 0;\n\n// reactions\nr1 @Reaction {actors: => p1} := vsyn;\n\n// parameters\nvsyn @Const = 0.1;\n"}
-{"prompt":" Create simple Heta model with constant synthesis of some metabolite. ","completion":"// index.heta\n\n// compartments\ncomp1 @Compartment .= 1;\n\n// species\nm1 @Species {compartment: comp1} .= 0;\n\n// reactions\nr1 @Reaction {actors: => m1} := vsyn;\n\n// parameters\nvsyn @Const = 0.1;\n\n// export\n#export {format: SBML};\n"}
-{"prompt":" Create simple model with reversible MM. Use short names for units like in qsp-units.heta ","completion":"// index.heta\n\n// list of units\n#defineUnit s {units: second};\n#defineUnit uM {units: (1e-6 mole)/litre};\n#defineUnit L {units: litre};\n#defineUnit umole {units: (1e-6 mole)};\n#defineUnit UL {units: dimensionless};\n\n// default time\nt {units: s};\n\n// compartment of size 1\ncomp1 @Compartment {units: L} .= 1;\n\n// substrate and product species\ns1 @Species {compartment: comp1, units: uM} .= 100;\np1 @Species {compartment: comp1, units: uM} .= 0;\n\n// reaction\nr1 @Reaction {actors: s1 -> p1, reversible: true, units: umole/s}; \nr1 := kcat * (s1 - p1/Keq) / (Km_s1 + s1 + Km_s1 / Km_p1 * p1) * comp1;\n\n// reaction constant\nkcat @Const {units: uM/s} = 0.1;\nKm_s1 @Const {units: uM} = 0.5;\nKm_p1 @Const {units: uM} = 1.1;\nKeq @Const {units: UL} = 10;\n\n// export format\n#export {format: SBML};\n"}
-{"prompt":" Create reversible MM kinetics model with 1 substrate and 1 product. Set units for all quantities without defineUnits. Units must be: second, micro moles, litre, etc. ","completion":"// index.heta\n\n// default time\nt {units: second};\n\n// compartment of size 1\ncomp1 @Compartment {units: litre} .= 1;\n\n// substrate and product species\ns1 @Species {compartment: comp1, units: (1e-6 mole)/litre} .= 100;\np1 @Species {compartment: comp1, units: (1e-6 mole)/litre} .= 0;\n\n// reaction\nr1 @Reaction {actors: s1 -> p1, reversible: true, units: (1e-6 mole)/second}; \nr1 := kcat * (s1 - p1/Keq) / (Km_s1 + s1 + Km_s1 / Km_p1 * p1) * comp1;\n\n// reaction constant\nkcat @Const {units: (1e-6 mole)/litre/second} = 0.1;\nKm_s1 @Const {units: (1e-6 mole)/litre} = 0.5;\nKm_p1 @Const {units: (1e-6 mole)/litre} = 1.1;\nKeq @Const {units: dimensionless} = 10;\n\n// export format\n#export {format: SBML};\n"}
-{"prompt":" Create simple model with reversible MM. Add units to all components from qsp-units.heta from default template. ","completion":"// index.heta\n\ninclude ./qsp-units.heta;\n\n// default time\nt {units: s};\n\n// compartment of size 1\ncomp1 @Compartment {units: L} .= 1;\n\n// substrate and product species\ns1 @Species {compartment: comp1, units: uM} .= 100;\np1 @Species {compartment: comp1, units: uM} .= 0;\n\n// reaction\nr1 @Reaction {actors: s1 -> p1, reversible: true, units: umole/s}; \nr1 := kcat * (s1 - p1/Keq) / (Km_s1 + s1 + Km_s1 / Km_p1 * p1) * comp1;\n\n// reaction constant\nkcat @Const {units: uM/s} = 0.1;\nKm_s1 @Const {units: uM} = 0.5;\nKm_p1 @Const {units: uM} = 1.1;\nKeq @Const {units: UL} = 10;\n\n// export format\n#export {format: SBML};\n"}
-{"prompt":" Create simple Heta model with reversible Michaelis-Menten (MM) kinetics. ","completion":"// index.heta\n\n// compartment of size 1\ncomp1 @Compartment .= 1;\n\n// substrate and product species\ns1 @Species {compartment: comp1} .= 100;\np1 @Species {compartment: comp1} .= 0;\n\n// reaction\nr1 @Reaction {actors: s1 -> p1, reversible: true}; \nr1 := Vmax * (s1 - p1 / Keq) / (Km_s1 + s1 + Km_s1 / Km_p1 * p1) * comp1;\n\n// reaction constant\nVmax @Const = 0.1;\nKm_s1 @Const = 0.5;\nKm_p1 @Const = 1.1;\nKeq @Const = 10;\n\n// export format\n#export {format: SBML};\n"}
-{"prompt":" Create simple Heta model with Michaelis-Menten (MM) type reaction for r1. ","completion":"// index.heta\n\n// compartment of size 1\ncomp1 @Compartment .= 1;\n\n// substrate and product species\ns1 @Species {compartment: comp1} .= 100;\np1 @Species {compartment: comp1} .= 0;\n\n// reaction\nr1 @Reaction {actors: s1 -> p1} := Vmax * s1 / (Km + s1) * comp1;\n\n// reaction constant\nVmax @Const = 0.1;\nKm @Const = 0.5;\n\n// export format\n#export {format: SBML};\n"}
-{"prompt":" Create simple kinetic model with two species and one reaction in Heta notation. Mass action kinetics is used. ","completion":"// index.heta\n\n// compartment of size 1\ncomp1 @Compartment .= 1;\n\n// substrate and product species\ns1 @Species {compartment: comp1} .= 100;\np1 @Species {compartment: comp1} .= 0;\n\n// reaction\nr1 @Reaction {actors: s1 -> p1} := k1 * s1 * comp1;\n\n// reaction constant\nk1 @Const = 0.1;\n\n// export format\n#export {format: SBML};\n"}
-{"prompt":" Create simple Heta model. For the same model add as many as possible available export options. ","completion":"// index.heta\n\n// compartment of size 1\ncomp1 @Compartment .= 1;\n\n// species with initial concentration 10\ns1 @Species {compartment: comp1} .= 10;\n\n// reaction of s1 degradation\nr1 @Reaction {actors: s1 => } := k1 * s1 * comp1;\n\n// constant of reaction\nk1 @Const = 0.01;\n\n// export format\n// another directory name, long format of units\n#export {format: JSON, filepath: xxx, noUnitsExpr: true};\n// long format of units\n#export {format: YAML, noUnitsExpr: true};\n// use pow(x, y) instead of x^y in the output, group constants by the first tag, use old format of SLV file\n#export {format: DBSolve, powTransform: function, groupConstBy: \"tags[0]\", version: 25};\n// use Level 3 version 2\n#export {format: SBML, version: L3V2};\n// another directory name for output directory\n#export {format: Simbio, filepath: yyy};\n// another directory name for output directory\n#export {format: Mrgsolve, filepath: zzz};\n// omit 3 rows between header and data, use multiple sheets in the output\n#export {format: Table, omitRows: 3, bookType: xlsx};\n// another directory name for output directory\n#export {format: Julia, filepath: www};\n// another directory name for output directory\n#export {format: Matlab, filepath: qqq};\n// another directory name for output directory\n#export {format: Dot, filepath: ppp};\n// another directory name for output directory\n#export {format: Summary, filepath: ooo};\n"}
-{"prompt":" Create simple Heta model. Add all available export formats with default file names and default options. ","completion":"// index.heta\n\n// compartment of size 1\ncomp1 @Compartment .= 1;\n\n// species with initial concentration 10\ns1 @Species {compartment: comp1} .= 10;\n\n// reaction of s1 degradation\nr1 @Reaction {actors: s1 => } := k1 * s1 * comp1;\n\n// constant of reaction\nk1 @Const = 0.01;\n\n// export format\n#export {format: JSON};\n#export {format: YAML};\n#export {format: DBSolve};\n#export {format: SBML};\n#export {format: Simbio};\n#export {format: Mrgsolve};\n#export {format: Table};\n#export {format: Julia};\n#export {format: Matlab};\n#export {format: Dot};\n#export {format: Summary};\n"}
-{"prompt":" Simple Heta model exported to SBML, JSON and YAML formats. ","completion":"// index.heta\n\n// compartment of size 1\ncomp1 @Compartment .= 1;\n\n// species with initial concentration 10\ns1 @Species {compartment: comp1} .= 10;\n\n// reaction of s1 degradation\nr1 @Reaction {actors: s1 => } := k1 * s1 * comp1;\n\n// constant of reaction\nk1 @Const = 0.01;\n\n// export format\n#export {format: SBML};\n#export {format: JSON};\n#export {format: YAML};\n"}
-{"prompt":" Create the simplest QSP model in Heta notation. Something like \"hello world\" in programming. One compartment, one species, one reaction with mass action. ","completion":"// index.heta\n\n// compartment of size 1\ncomp1 @Compartment .= 1;\n\n// species with initial concentration 10\ns1 @Species {compartment: comp1} .= 10;\n\n// reaction of s1 degradation\nr1 @Reaction {actors: s1 => } := k1 * s1 * comp1;\n\n// constant of reaction\nk1 @Const = 0.01;\n\n// export format\n#export {format: SBML};\n"}
+{"prompt":" Create simple Heta model with constant synthesis of some metabolite. ","completion":"// index.heta\n\n// compartments\ncomp1 @Compartment .= 1;\n\n// species\nm1 @Species {compartment: comp1} .= 0;\n\n// reactions\nr1 @Reaction {actors: => m1} := vsyn;\n\n// parameters\nvsyn @Const = 0.1;\n"}
+{"prompt":" Create simple model with reversible MM. Use short names for units like in qsp-units.heta ","completion":"// index.heta\n\n// list of units\n#defineUnit s {units: second};\n#defineUnit uM {units: (1e-6 mole)/litre};\n#defineUnit L {units: litre};\n#defineUnit umole {units: (1e-6 mole)};\n#defineUnit UL {units: dimensionless};\n\n// default time\nt {units: s};\n\n// compartment of size 1\ncomp1 @Compartment {units: L} .= 1;\n\n// substrate and product species\ns1 @Species {compartment: comp1, units: uM} .= 100;\np1 @Species {compartment: comp1, units: uM} .= 0;\n\n// reaction\nr1 @Reaction {actors: s1 -> p1, reversible: true, units: umole/s}; \nr1 := kcat * (s1 - p1/Keq) / (Km_s1 + s1 + Km_s1 / Km_p1 * p1) * comp1;\n\n// reaction constant\nkcat @Const {units: uM/s} = 0.1;\nKm_s1 @Const {units: uM} = 0.5;\nKm_p1 @Const {units: uM} = 1.1;\nKeq @Const {units: UL} = 10;\n"}
+{"prompt":" Create reversible MM kinetics model with 1 substrate and 1 product. Set units for all quantities without defineUnits. Units must be: second, micro moles, litre, etc. ","completion":"// index.heta\n\n// default time\nt {units: second};\n\n// compartment of size 1\ncomp1 @Compartment {units: litre} .= 1;\n\n// substrate and product species\ns1 @Species {compartment: comp1, units: (1e-6 mole)/litre} .= 100;\np1 @Species {compartment: comp1, units: (1e-6 mole)/litre} .= 0;\n\n// reaction\nr1 @Reaction {actors: s1 -> p1, reversible: true, units: (1e-6 mole)/second}; \nr1 := kcat * (s1 - p1/Keq) / (Km_s1 + s1 + Km_s1 / Km_p1 * p1) * comp1;\n\n// reaction constant\nkcat @Const {units: (1e-6 mole)/litre/second} = 0.1;\nKm_s1 @Const {units: (1e-6 mole)/litre} = 0.5;\nKm_p1 @Const {units: (1e-6 mole)/litre} = 1.1;\nKeq @Const {units: dimensionless} = 10;\n"}
+{"prompt":" Create simple model with reversible MM. Add units to all components from qsp-units.heta from default template. ","completion":"// index.heta\n\ninclude ./qsp-units.heta;\n\n// default time\nt {units: s};\n\n// compartment of size 1\ncomp1 @Compartment {units: L} .= 1;\n\n// substrate and product species\ns1 @Species {compartment: comp1, units: uM} .= 100;\np1 @Species {compartment: comp1, units: uM} .= 0;\n\n// reaction\nr1 @Reaction {actors: s1 -> p1, reversible: true, units: umole/s}; \nr1 := kcat * (s1 - p1/Keq) / (Km_s1 + s1 + Km_s1 / Km_p1 * p1) * comp1;\n\n// reaction constant\nkcat @Const {units: uM/s} = 0.1;\nKm_s1 @Const {units: uM} = 0.5;\nKm_p1 @Const {units: uM} = 1.1;\nKeq @Const {units: UL} = 10;\n"}
+{"prompt":" Create simple Heta model with reversible Michaelis-Menten (MM) kinetics. ","completion":"// index.heta\n\n// compartment of size 1\ncomp1 @Compartment .= 1;\n\n// substrate and product species\ns1 @Species {compartment: comp1} .= 100;\np1 @Species {compartment: comp1} .= 0;\n\n// reaction\nr1 @Reaction {actors: s1 -> p1, reversible: true}; \nr1 := Vmax * (s1 - p1 / Keq) / (Km_s1 + s1 + Km_s1 / Km_p1 * p1) * comp1;\n\n// reaction constant\nVmax @Const = 0.1;\nKm_s1 @Const = 0.5;\nKm_p1 @Const = 1.1;\nKeq @Const = 10;\n"}
+{"prompt":" Create simple Heta model with Michaelis-Menten (MM) type reaction for r1. ","completion":"// index.heta\n\n// compartment of size 1\ncomp1 @Compartment .= 1;\n\n// substrate and product species\ns1 @Species {compartment: comp1} .= 100;\np1 @Species {compartment: comp1} .= 0;\n\n// reaction\nr1 @Reaction {actors: s1 -> p1} := Vmax * s1 / (Km + s1) * comp1;\n\n// reaction constant\nVmax @Const = 0.1;\nKm @Const = 0.5;\n"}
+{"prompt":" Create simple kinetic model with two species and one reaction in Heta notation. Mass action kinetics is used. ","completion":"// index.heta\n\n// compartment of size 1\ncomp1 @Compartment .= 1;\n\n// substrate and product species\ns1 @Species {compartment: comp1} .= 100;\np1 @Species {compartment: comp1} .= 0;\n\n// reaction\nr1 @Reaction {actors: s1 -> p1} := k1 * s1 * comp1;\n\n// reaction constant\nk1 @Const = 0.1;\n"}
+{"prompt":" Create the simplest QSP model in Heta notation. Something like \"hello world\" in programming. One compartment, one species, one reaction with mass action. ","completion":"// index.heta\n\n// compartment of size 1\ncomp1 @Compartment .= 1;\n\n// species with initial concentration 10\ns1 @Species {compartment: comp1} .= 10;\n\n// reaction of s1 degradation\nr1 @Reaction {actors: s1 => } := k1 * s1 * comp1;\n\n// constant of reaction\nk1 @Const = 0.01;\n"}