How to reference compartment value? (Volume)

How do I reference the volume of a compartment in a mathematical expression?

For example, I can reference species "S" in compartment "C" via:

C.S

But none of these works to reference C's volume, even though they are the properties of compartments according to the documentation :

C
C.capacity
C.value

I can't seem to find an answer in the documentation.

Answer 1

[Jeremy Huard]

Hi Felix,

you can refer to the volume of a compartment by the name of the compartment in any expression: C in your case.

Here is a quick example:

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

[Felix]

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]

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

I am curious about your use case though.

Can you tell me more about the what you are trying to achieve?

Best regards,

Jérémy