Mihail Anton

Here are some very specific questions and observations - please excuse my ignorance and silly questions: - the `tsv` is inconsistent in its use of quotations `"` - is it...

> What is the status of this? This is a bit of a thorny issue. I don't think I can remember all the details accurately (please correct me @edkerk @pecholleyc...

I should have mentioned this, but Metabolic Atlas is relying on the `subsystem` field in the `yml` populate the reaction-subsystem association. We will likely have to postpone updating the model...

@edkerk I'm following up on your questions below. > But it makes sense that this information is sourced from subsystem in the yml? I guess we can also change how...

I fully support/encourage automatic mapping of EC numbers. A good way to map to MNX would be via Rhea IDs; however, these are missing from the model annotation, so then...

> Could you say something about how you would expect to provide this information? It seems a bit intricate just for command line arguments so maybe a config file? What...

> no longer required as invalid IDs would already have thrown an error. @edkerk this got me thinking - are invalid reported throwing errors for _all_ import formats, including `importExcelModel`?

Resolving the conflict and the merging of #364 brings this PR in a merge-able state. > Release 2.5.4 has then minor changes, while release 2.6.0 (this PR) will have the...

Good catch @simas232. > this is definitely problematic for GEMs that use BiGG IDs for `mets` and/or `rxns`. To me, this sounds very much like a problem with the GEMs...

Preserving the detailed history might be too hard and potentially unnecessary, so I'm thinking an option would be to copy over several intermediate versions and commit these while [specifying the...