#22 Compartment size could be absent

[Chen]

Hello,

I have a model, which compartment was not used by any species or reactions.

For instance, in the model I attached, its species has intialAmount and hasOnlySubstanceUnits is TRUE. The whole model's reactions doesn't nothing with the compartment. For this model, it should be able to be simulated without given compartment size.

Regards,
Chen

[Chen]

[Nobody/Anonymous]

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hi Chen:

Looks like SOSlib returns a fatal error message "No value found for compartment cell" in this case?

BTW, it seems MathSBML integrates the model correctly, but it does so with the complaint that value for compartment is absent.

James

[Chen]

Logged In: YES
user_id=1712101
Originator: YES

Hi, James,

> Looks like SOSlib returns a fatal error message "No value found for
> compartment cell" in this case?

Yes, I got that error. In this model, all reactions do nothing with that compartment. It was there, only because species need to be defined in at least one compartment according to SBML spec.

So in this case, my humble opinion is, SOSlib should not throw that error.

Regards,
Chen