Mihail Anton

As Metabolic Atlas relies on the YAML file to import models, all of the proposed changes would lead to breaking the import of models. Here are my thoughts on the...

> In addition, it would be good to have a `checkIDvalidity` function (or other name?) that runs a few regexp on `model.mets`, `model.rxns` and `model.comps`, to ensure that they adhere...

There are many different options to handle the exceptions introduced by SBML. For me, uniformity and absence of surprises are important. This is why I really like that: > I/O...

Instead of `COBRAstyle` as a parameter, how about the following scenario: exporting an incompatible model crashes `exportModel` with a message asking the user to run a function called `makeIdsSBMLFriendly`, which...

Thank you for the question @Selimvrl. There have been long-standing issues regarding the reaction names, and only incremental have been made so far in https://github.com/SysBioChalmers/Human-GEM/issues/333 and https://github.com/SysBioChalmers/Human-GEM/issues/181. If your question...

Looking a bit more into this, the annotation for these reactions doesn't look straightforward. A name search for `(S)-dihydroorotate` returned [CHEBI:30864](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30864), but that is different from [CHEBI:17025](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17025) which is the...

> I came across this one accidentally, but I am wondering if there is any automatic way to do these checkings and update the model once in a while? That's...

While I fully support the idea behind this issue, I don't have a straightforward suggestion here. It feels like there is no "ground truth" database to be used for the...

I'm at the point where I think _any_ names would be better than the 8000+ reactions with no names. One way to do this would be to fetch the names...

I hope it's okay to ping @haowang-bioinfo and @JonathanRob to discuss the idea mentioned above: reactions in KEGG have names. Would it make sense to programmatically use KEGG as a...