Eduard Kerkhoven

Addressed in #191

Did you use the same DLKcat output file to make both a light and full ecModel?

Indeed, this check is to make sure that the `kcatList` can later be used by `selectKcatValue`, which just matches by reaction ID: https://github.com/SysBioChalmers/GECKO/blob/1710a9861a60249207d547585cc96581e0ece18b/src/geckomat/gather_kcats/selectKcatValue.m#L51 Short term solution is to have the...

Mentioned in the protocol. Longer term goal would be to enhance the parsing of the file, to avoid this.

No reason to avoid gene ID, that is actually my plan, to map by the core of the reaction ID (so without prefixes and suffixes from _light_ and _full_ ecModels)...

As mentioned above, human-GEM is a large model, while ftINIT is a complex approach, so it indeed heavily depends on an well-functioning solver. Gurobi is superior in that aspect, so...

Could you please specify (or link) which model file you exactly used?

Included in #339

Hmm, even if `saveYeastModel` is changed, it would still produce a valid SBML file that cobrapy should be able to import without issues. Just to confirm that it is really...

I went through all suggested reactions, checked them one-by-one. With the quality of the current yeast-GEM, one should be careful to include new reactions, there should be more evidence than...