Mihail Anton

For `Uppmax` #53 and `Hebbe` #54 the CI seems to report the same issue. Is there a mismatch between the documentation and the changes in the PRs?

> * Stoichiometry coefficients are missing in current GEM but available in Complex Portal and PDB database. I'm really unsure about which coefficients this discussion is about, could you give...

> This would for instance make a difference if the model would be turned into an ec-model, but there are likely also other use cases. Thanks for the example @edkerk....

I'm very hesitant to "copy" external data in any repository, unless it would be useful for a good chunk of the userbase. > also ready for other applications? I see...

Based on the experience with Human-GEM, I can recommend using MNXref. Alternatively, BridgeDB might be worthwhile to look into. edit: sorry about accidentally closing the issue

Great to see this @edkerk. > * Reduce software dependencies for contributing to model development. Any thoughts on the `/requirements` folder?

@edkerk coming back to the `/requirements` folder, one idea could be to move it under `/code`. To me, it belongs there more. If it were used just by GH Actions,...

> `requirements/` is now moved to `code/requirements/` in [dcf1cae](https://github.com/SysBioChalmers/yeast-GEM/commit/dcf1cae74919a169640252beed2cb7f7ebc7bddd) very nice @edkerk. I think there are more place that should be updated, such as the [Contributing guidelines](https://github.com/SysBioChalmers/yeast-GEM/blob/main/.github/CONTRIBUTING.md#managing-python-dependencies).

I would suggest looking into an automatic way of keeping annotation updated.

Is there any timeline for this change, at least with regards to having this up on a feature branch?