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biosimulators / Biosimulators_GillesPy2

GillesPy2 biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
https://docs.biosimulators.org/Biosimulators_GillesPy2
MIT License
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Are all of the results (predictions) for species? #14

Closed jonrkarr closed 3 years ago

jonrkarr commented 3 years ago

@briandrawert To support SED-ML, we need to know the SBML XPATH of each recorded result. Are the results always predictions of species?

More specifically, do the keys of results_dict

_, results_dict = model.run(solver, ...)

map to these XPATHs?

/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='{ key-of-results_dict }']
jonrkarr commented 3 years ago

I now see that GillesPy2 records everything it interprets as a species, including parameters set via assignment rules. GillesPy2 tracks that ids of each object it interprets as a species.

In general, the XML file must be read to map XPATHs to object ids. But it most cases, SED-ML files use XPATHs that involve the ids. Currently, this package only supports such XPATHs. This enables this package to link XPATHs to the ids that GillesPy2 uses without having to read the SBML file.

This limitation should be removed so that XPATHs aren't limited to this convention.

jonrkarr commented 3 years ago

I implemented the above with a new method in biosimulators-utils. The error messages could still be more informative, but the problem is basically addressed now.