Event error after updating model with BasiCO

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Theo Redfern

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Sep 4, 2023, 8:09:59 AM9/4/23
to COPASI User Forum
Hey everyone,

There's a possible bug I've found after you update a model with BasiCO:

I made a model with the COPASI GUI. Then I needed to append some reactions to this model and add in some parameters. After loading the model, adding the reactions and parameters I saved the model, using your wonderful BasiCO python package, I then found an error. This error pops up when loading the model back again with the COPASI GUI.

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Problem while loading file /my/copasi/files/02_Data/03_Models/02_A2AR_Models/02_Extended_A2AR_Model_v01.cps!


>WARNING 2023-09-04T13:00:17<

Invalid EventAssignment for 'CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[L],Reference=Concentration': object does not exist.

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This is particularly odd as I haven't changed or updated the event with BasiCO at all!


(I also always get this error message when opening a BasiCO-adapted or BasiCO-created model with the COPASI GUI):

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>WARNING 2023-09-04T13:00:17<

XML (9): The content is created with a newer version '4.41.280 (Source)' of COPASI.

This means it might include features your version of COPASI does not support.

To assure full compatibility please download the newest version at http://www.copasi.org.

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Yet I think I have the most updated COPASI version 4.40.278?


I don't particularly mind either of these errors as they are easily fixed or easily ignored. But just thought I'd flag them in case I might be doing something wrong, or in case they are useful to you!


Thanks for all your brilliant work developing COPASI!

Best,

Theo

Frank Bergmann

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Sep 5, 2023, 9:20:54 AM9/5/23
to COPASI User Forum
Hello Theo, 

do you think you could (perhaps privately share the model code creating the model, or perhaps the broken file)? 

What I believe is happening here, is that the newer version of COPASI that is being used by the python bindings (and for which we didn't release a GUI update yet), has an update that can be used for event assignments to target particle numbers instead of concentrations. It seems to me that when loading this back into a COPASI that didn't have the feature, the warning is created. The question is whether the simulation still worked as planned. 

Thanks for letting us know, 
best
Frank

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