Mihail Anton

Just a note, the above is without having exposed a purpose-built API. Therefore, my recommendation would be to see that as a foundation to build a more compact and potentially...

Here is the link to the promised API https://metabolicatlas.org/api/v2/#/GotEnzymes

It sounds to me like this could also sit within `ecModels`, continuing the idea of separating GECKO as a tool from its applications. My attempt to solve the loading of...

> since the second request is always returned from **cache** On the latest Firefox (macOS) I do see the data _transferred twice_, so, as @kito-inv mentioned above, it's not cached....

Bumping this as it is still unresolved for Firefox.

Just to make sure, you ran the same code, including the same data (DLD1 from Hart2015 from within the `data/datasets` folder. Was this tINIT or the newer [ftINIT](https://sysbiochalmers.github.io/Human-GEM-guide/gem_extraction/)? Also, are...

> I'm sure I used the same code and data. This was tINIT. I only ran the code twice within 24 hours, and I believe that the Human-GEM version didn't...

@yangjingyu1108, here is a starting point for a longer discussion on the "consistency" of model contextualization/extraction algorithms that, e.g., use either random order of pruning reactions or random seeds in...

> It might be better to take steps by starting with adding a dedicated file for storing SMILES for prototyping, and merging to `metabolites.tsv` later. > I say the file...

Very good point @JonathanRob. I want to remember someone sharing a story about this, something like starting to map via SMILES because it was easier/more popular in other databases, and...