Eduard Kerkhoven

I'm not sure why, but the `geneFrom` field (which is inherited from the template model) has less entries than the number of genes in the new model. Regardless, the `geneFrom`...

Failing tests is likely due to invalid gurobi license on the CI server.

@haowang-bioinfo You mean have 1 commit for each ID that is changed?

Many of the reactions involve cytochrome P450s, which can often can take quite a few different substrates, so that a very thorough curation would be required to further clean this...

To my knowledge, there is no active development around Yeast-GEM visualization. DD-DeCaF is no longer functional, [MetabolicAtlas](https://metabolicatlas.org/explore/Yeast-GEM/map-viewer/) has some yeast maps, but these are mostly suited for overlaying omics data,...

Well spotted, and thanks for reporting. It would indeed make sense to write a function to identify potential incorrect reactions. For those two reactions specifically though, the use of the...

Indeed, I think it is two separate questions: 1. Are the current peptide reactions correct? No -> @pranasag fixed this in #839 2. Should peptide reactions be in the model...

Indeed, the rational can then be that "human-GEM contains di- and tripeptides as reported in HMDB", while others not in that database will be removed (unless there is very strong...

It hasn't been specifically tested with other solvers, it was designed for Gurobi. Which alternative solver do you have in mind?

As shown in the memote workflow referred to in the previous comment, cobrapy can read the `Human-GEM.yml` file directly with `model = cobra.io.load_yaml_model("model/Human-GEM.yml")`. At the same time, on my PC...