Using simFunction Object in Simbiology when my stoichiometry depends on a model parameter

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Mehdi
Mehdi 2024-3-21
回答： Arthur Goldsipe 2024-3-21
Hi,
Prevusly asked this question and my problem was solved. Now I have another question:
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I am working on a SimBiology code with Stochiometry depending on a parameter (DAR). The specise are calculated based on their concentrations (nmol/liter). The size of the component changes too which is based on repeated rules. I use SimFunction for paarmetrization, therefor as we discussed, I use rate rules for the specieses in which their concentration depends on DAR. The method was explained before in this thread. But I get the follwoing error. Is their any way to fix this error?
Rate rule for species 'PL_ext' is invalid. Species 'PL_ext' is in concentration and in a compartment with varying capacity. For this to be valid, the compartment capacity
must be varied by a rate rule.

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Arthur Goldsipe
Arthur Goldsipe 2024-3-21
The error you report is intended to communicate that SimBiology does not allow the following the following combination of conditions:
  • A species is in concentration.
  • The concentration of that species is determined by a rate rule.
  • The compartment (that the species is in) is determined by a repeated assignment rule or an algebraic rule.
One fix would be the one mentioned at the end of the error message: Replace the repeated assignment rule or algebraic rule with a rate rule that gives equivalent behavior.
Another option would be to change the species units to amount instead of concentration and use (species amount)/(compartment volume) anywhere you need to reference the concentration.

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