Jonathan Robinson

Do you mean the FFAs would be isolated in the sense that they no longer are associated with any reactions? If so, then I think it would be fine to...

Really enjoying this clean-up of the beta-oxidation reactions. This looks good to me. Out of curiosity, and maybe I missed it before, are you using a script-based approach to search...

Ok, great work though.

I agree with @mihai-sysbio to first check for any changes in model version, repo version, etc. If everything is exactly the same, there is still a possibility that tINIT can...

@JHL-452b SMILES unfortunately suffers from the lack of a canonical (unique) code for a given molecule - i.e., the same molecule can often be described with different SMILES. It is,...

If SMILES really are more frequently used and would simplify mapping, then I would support adding them. I just assumed that they were essentially made obsolete by InChIs due to...

Really nice work @Devlin-Moyer. What do you think about the fact that by removing the direct ubiquinone-reducing reaction, the mechanism can instead use another electron acceptor to oxidize FADH2? I...

> Although I now notice that SDHA is listed as one of the only the 6 human flavoenzymes that covalently bind their FAD, and SDHA catalyzes MAR04652 and MAR08743, so...

Thanks for the description, @e0. Now I understand why the reactants were named "outgoing" metabolites. I agree with @haowang-bioinfo - if possible, it would be nice to just use the...

Even though it shows a ton of unconserved metabolites and a very low stoichiometric consistency, it could be as simple as one reaction being unbalanced. I would recommend taking a...