Zak King

I have a related use case that supports adopting compartments as a first-class entity. We are trying to use COBRApy as much as we can within our web-based reconstruction tool....

I suggest extending the COBRApy JSON-schema for models to explicitly define the data structure. That will make it much easier for users to parse & validate. As long as the...

Depends on the goals for the schema project. I have no problem with it being inside of COBRApy, since that's the source of those files

Probably the quickest way to get changes into Escher right now is to open a PR. I’m happy to merge and sort out how to do a new release (it’s...

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...

Specifically, it would be nice to download all the models at once from a page. Maybe this should be publication specific? or species specific. We should also consider grouping the...

that's a good idea. like a "top models" tag

Thanks for making an issue for this. These identifiers are in SBML, but we should also include them in JSON model downloads and on the Data Access page (e.g. with...

This is a good idea, and we did have discussion on it previously: https://github.com/SBRG/bigg_models/issues/145 The challenge is, or course, the effort required for manual curation. We have generally avoided manual...

Yes, I think that's a great idea. We have to be careful with the licensing of the models (hence the "BiGG License"), but for identifiers it's not an issue and...