Load SimBiology to COPASI

[Grzegorz Bokota]

Hello,

I would like to load into COPASI an SBML model which comes from this article https://www.frontiersin.org/articles/10.3389/fbioe.2020.00141/full. This model has been created in Matlab with SimBiology plugin and exported to SMBL. The loading of the model fails because some of the subelements of kineticLaw are not listed in the listOfReactants, listOfProducts or listOfModifiers.

I've got information from the authors that this is a well-known problem that when exporting from SimBiology the listOfModifiers is not filled. I have created a script that updates the model with the missing elements. 

With the current state of the model, I could load it into COPASI but with warnings like:

>WARNING 2021-09-09T21:38:19<

SBML (79): COPASI was not able to handle the substance unit for species with id "mwb86eb755_5b57_4338_b9db_0d5da84f0b05". The unit has been ignored.

Does anyone have any suggestions how I can proceed to fix this? Are there any instructions/tutorials on how to load SImBiology SBML to COPASI? Or how to transform such a model so that would work?

I am attaching the original model and the version updated by my script.

Regards,

Grzegorz Bokota

[sven....@gmail.com]

Dear Grzegorz,

without having looked at the specific model, generally the units in an SBML file are only a documentation/annotation of the modelers intent. Software (like COPASI) can use this information, e.g. to check consistency, but it should have no impact on the numbers of the simulation. I.e. the actual simulation should run correctly without knowing the units, and the units are only useful for you to understand what the numbers mean. 

So, if the rest of the conversion was successful, you could just use the numbers generated from COPASI and interpret them using the units as documented in the paper.

Sven

[Frank Bergmann]

Hello, 

just wanted to chime in as to why you see these warnings, in COPASI we made the decision to use one unit for the species (similarly all 3d compartments have the same units and so on). That way it is easier to keep models consistent. The model here uses different units for species, and 3d compartments, and that is why you see the warnings. 

That being said, as pointed out by sven this will not influence the numerical calculations, just the display of the units within COPASI will be different. 

best

Frank

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