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The BiGG Models website server
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universal_model.json re sbml writing and metabolite formulas #299

Open maureencarey opened 6 years ago

maureencarey commented 6 years ago

Hi - I am building models using the universal model (accessed here: http://bigg.ucsd.edu/data_access as universal_model.json) but cannot write the universal model as an SBML file using CobraPy's write_sbml_model. I'm using CobraPy 0.13.0, python 3.6.4, and cobra.io.write_sbml_model(universe_model, "universe_model.xml").

Is there another version of the universal model that would be better suited for this purpose?

Also, I've detected a few metabolites can be produced erroneously - to test for mass imbalances, I turned off inward exchange and optimized for a demand reaction for each metabolite. I got a few metabolites that could be synthesized this way, but I only ran this for about a third of the metabolites in the model. Due to some numerical issues on my end testing all of them, it's hard to detect the 'problem' reactions. These mass imbalances can be biologically feasible in certain contexts, but I was wondering if there was a version of the universal model that excluded those reactions or included metabolite formulas for easier detection.

Thanks!

zakandrewking commented 6 years ago

The SBML export is an issue with COBRApy—or our implementation of it on BiGG—so see this new issue for progress on fixing it: https://github.com/opencobra/cobrapy/issues/736

We don't have a universal model that can help with those things now, but I'll leave this open so we can consider improvements.

maureencarey commented 6 years ago

thank you for the info!