These are chat archives for opencobra/cobrapy

11th
Aug 2017
Henning Redestig
@hredestig
Aug 11 2017 00:20
yeah, not as dependency for sure, but perhaps facilitate using. In one of our applications we have some silly issues with conveniently fetching the cobra metabolites that correspond to a given chemical compound.
Peter St. John
@pstjohn
Aug 11 2017 02:29
I'm guessing you'll go through metanetX to get to kegg or metacyc smiles/inchi? and then you might also run into the issue of protonation state..
Henning Redestig
@hredestig
Aug 11 2017 11:25
yes it's not hard, just a bit awkward that there is no dedicated property for a compound identifier (that isn't compartment dependent) associated with the metabolite.
João Gonçalo Rocha Cardoso
@joaocardoso
Aug 11 2017 12:22
@pstjohn hi! We have a package for data-oriented modeling called driven (https://driven.bio). Not as developed as cameo, unfortunately. It was meant to include all sorts of data integration (metabolite concentration, transcriptomics, etc.)
Mike Mundy
@mmundy42
Aug 11 2017 13:45
I recently updated CobraBabel to support the latest MetaNetX version. The SMILES, InChI, and InChIKey data are included as notes in the Metabolite objects.