Utilization of COBREXA.jl

[paulflang]

Using COBREXA.jl❓

Will this repo utilize https://lcsb-biocore.github.io/COBREXA.jl/stable/ for flux balance analysis?

[vyudu]

Admittedly I haven't thought that far ahead about this -- implementing FBA was just something that came to mind as a possible addition because I was thinking about how to compute elementary flux modes. It does seem like COBREXA does all of that already though (thanks for the heads up), so it doesn't seem like there's any reason to have it in this package too.

Just learning about COBREXA -- does it work with Catalyst's ReactionSystem as well as an import format? If not that could be some functionality to think about.

[paulflang]

Well, last time I checked Catalyst uses rate laws on reactions, not flux bounds. So I don't see how you can directly use it for FBA. But of course, you could ignore rate laws and add flux bounds instead. But I don't see use cases for that. Also, you don't want to write converters between tools directly, but converters to and from a shared standard (turns an n*m problem into a n+m problem). I think the standard to use here is SBML. There is already COBREXA and Catalyst import, but at least the Catalyst to SBML exporter is still missing. I don't have the time to write it, but happy to give guidance if anyone is interested.

Anyway, looking forward to seeing how the dynamic analysis develops.

(Also, feel free to join the #sciml-sysbio channel on the Julia Slack and the sysbio community call mailing list for help and further discussion, if you are not on these channels yet 🙂)