How to reference compartment value? (Volume)

modelObj = sbiomodel('model');
compObj = addcompartment(modelObj,'C',1,Units='liter');
addspecies(compObj,'S',0,Units='milligram/liter');
addparameter(modelObj,'ke',0,Units='1/hour');
addparameter(modelObj,'CL',2,Units='liter/hour');
addrule(modelObj,'ke = CL/C','initialAssignment');
reacObj = addreaction(modelObj,'C.S -> null');
kObj = addkineticlaw(reacObj,"MassAction");
kObj.ParameterVariableNames = {'ke'};
cs = getconfigset(modelObj);
cs.CompileOptions.UnitConversion = true;
modelObj.Rules
ans = 
   SimBiology Rule Array

   Index:    RuleType:            Rule:    
   1         initialAssignment    ke = CL/C

Best regards,

Jérémy

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Felix 2022-9-23

It seems I can't reference the compartment volume as a stoichiometric coefficient in the model builder. Any idea how I can do that?

Since my original question has been answered I will accept this answer, thank you!

Jeremy Huard 2022-9-29

在 MATLAB Online 中打开

Hi Felix,

stoichiometric coefficients must be numbers (double) and they can't be parametrized. Which means that a reaction like

is fine but

is not.

One way to achieve this woud be with a script that modifies the stoichiometric coefficient. For example:

modelObj = sbiomodel('cell');
compObj = addcompartment(modelObj,'Central',10,Units='liter');
reactionObj = addreaction(modelObj, '2 a + b -> c');
modelObj.Reactions
ans = 
   SimBiology Reaction Array

   Index:    Reaction:   
   1         2 a + b -> c
reactionObj.Stoichiometry(2) = -compObj.Value;
modelObj.Reactions
ans = 
   SimBiology Reaction Array

   Index:    Reaction:      
   1         2 a + 10 b -> c