update cases to use the not in Chat mode

hetalang · Jun 16, 2024 · a6f3cfb · a6f3cfb
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diff --git a/cases/0001/index0.heta b/cases/0001/index0.heta
@@ -1,6 +1,7 @@
 /*
     Create the simplest QSP model in Heta notation.
     Something like "hello world" in programming.
+    One compartment, one species, one reaction with mass action.
 */
 // index.heta
 

diff --git a/cases/0001/index1.heta b/cases/0001/index1.heta
@@ -1,5 +1,5 @@
 /*
-    Add another simple export formats
+    Simple Heta model exported to SBML, JSON and YAML formats.
 */
 // index.heta
 

diff --git a/cases/0001/index2.heta b/cases/0001/index2.heta
diff --git a/cases/0001/index3.heta b/cases/0001/index3.heta
diff --git a/cases/0001/index4.heta b/cases/0001/index4.heta
@@ -1,4 +1,5 @@
 /*
+    Create simple Heta model.
     Add all available export formats with default file names and default options.
 */
 // index.heta

diff --git a/cases/0001/index5.heta b/cases/0001/index5.heta
@@ -1,4 +1,5 @@
 /*
+    Create simple Heta model.
     For the same model add as many as possible available export options.
 */
 // index.heta

diff --git a/cases/0002/index1.heta b/cases/0002/index1.heta
@@ -1,5 +1,5 @@
 /*
-  Use Michaelis-Menten type reaction for r1.
+  Create simple Heta model with Michaelis-Menten (MM) type reaction for r1.
 */
 // index.heta
 

diff --git a/cases/0002/index2.heta b/cases/0002/index2.heta
@@ -1,5 +1,5 @@
 /*
-  Replace non-reversible Michaelis-Menten (MM) kinetics by reversible Michaelis-Menten kinetics.
+  Create simple Heta model with reversible Michaelis-Menten (MM) kinetics.
 */
 // index.heta
 
@@ -12,7 +12,7 @@ p1 @Species {compartment: comp1} .= 0;
 
 // reaction
 r1 @Reaction {actors: s1 -> p1, reversible: true}; 
-r1 := Vmax * (s1 - p1/Keq) / (Km_s1 + s1 + Km_s1 / Km_p1 * p1) * comp1;
+r1 := Vmax * (s1 - p1 / Keq) / (Km_s1 + s1 + Km_s1 / Km_p1 * p1) * comp1;
 
 // reaction constant
 Vmax @Const = 0.1;

diff --git a/cases/0002/index3.heta b/cases/0002/index3.heta
@@ -1,6 +1,6 @@
 /*
-  Add units to all components.
-  Units can be taken from qsp-units.heta from default template.
+  Create simple model with reversible MM.
+  Add units to all components from qsp-units.heta from default template.
 */
 // index.heta
 

diff --git a/cases/0002/index4.heta b/cases/0002/index4.heta
@@ -1,5 +1,6 @@
 /*
-  Do not use units from qsp-units.heta. Use only base units.
+  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.
 */
 // index.heta
 

diff --git a/cases/0002/index5.heta b/cases/0002/index5.heta
@@ -1,4 +1,5 @@
 /*
+  Create simple model with reversible MM.
   Use short names for units like in qsp-units.heta
 */
 // index.heta

diff --git a/cases/0003/index1.heta b/cases/0003/index1.heta
@@ -1,6 +1,6 @@
 /*
-    Remove export.
-    Rename species to p1.
+    Do not use export action.
+    Create Heta model for constant production of species p1 in compartment comp1.
 */
 // index.heta
 

diff --git a/cases/0003/index2.heta b/cases/0003/index2.heta
diff --git a/cases/0003/index3.heta b/cases/0003/index3.heta
@@ -1,5 +1,5 @@
 /*
-    Make s1 buffered (boundary) which means s1 does not change in time.
+    Create Heta model where product is transformed from boundary (buffered) species.
 */
 // index.heta
 

diff --git a/cases/0003/index4.heta b/cases/0003/index4.heta
@@ -1,5 +1,6 @@
 /*
-    Put s1 and p1 into two different compartments
+    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.
 */
 // index.heta
 
@@ -8,11 +9,11 @@ comp1 @Compartment .= 1;
 comp2 @Compartment .= 3;
 
 // species
-p1 @Species {compartment: comp1} .= 0;
-s1 @Species {compartment: comp2, boundary: true} .= 100;
+s1 @Species {compartment: comp1, boundary: true} .= 100;
+p1 @Species {compartment: comp2} .= 0;
 
 // reactions
-r1 @Reaction {actors: s1 => p1} := k1 * s1 * comp2;
+r1 @Reaction {actors: s1 => p1} := k1 * s1 * comp1;
 
 // parameters
 k1 @Const = 0.1;
diff --git a/cases/0004/index1.heta b/cases/0004/index1.heta
@@ -1,5 +1,5 @@
 /*
-    Use stoicheometry 2 for the species
+    Create Heta model where substrate is eliminagted with stoichiometry 2.
 */
 // index.heta
 

diff --git a/cases/0004/index2.heta b/cases/0004/index2.heta
@@ -1,5 +1,5 @@
 /*
-    Add product with stoicheometry 1
+    Write Heta model with reaction where substrate is transformed to product with stoichiometry 2:1.
 */
 // index.heta
 

diff --git a/cases/0004/index3.heta b/cases/0004/index3.heta
@@ -1,5 +1,5 @@
 /*
-    Create a model with a single compartment, and reaction with stoicheometry
+    Create a Heta model with a single compartment, and reaction with stoicheometry
     2s1 + 3s2 => p1 + p2 
 */
 // index.heta

diff --git a/cases/0004/index4.heta b/cases/0004/index4.heta
@@ -1,5 +1,6 @@
 /*
-    Make reaction reversible
+    Create Heta model with reversible reaction and stoicheometry: 2s1 + 3s2 <=> p1 + p2.
+    Use mass action law.
 */
 // index.heta
 

diff --git a/cases/0004/index5.heta b/cases/0004/index5.heta
@@ -1,6 +1,7 @@
 /*
-    Ad units of measurments for all.
-    Use short designation for units
+    Create Heta model with reversible reaction and stoicheometry: 2s1 + 3s2 <=> p1 + p2.
+    Use mass action law.
+    Define units for time, volume, and concentration.
 */
 // index.heta