MICOM database to build model

[suetli19]

Hi,

I'm wondering if the micom built function is compatible with the APOLLO genome-scale metabolic reconstruction database and if this can be incorporated into micom? Here's the link to the paper that develops APOLLO - https://www.cell.com/cell-systems/fulltext/S2405-4712(25)00029-8

I find that the AGORA2 database has some issues with reading SBML files and some of the strains that I need were not in the database.

Thank you.

[cdiener]

Compatible yes, but we don't provide a prebuilt model database for it right now. It's a good idea though and I will try to include the APOLLO+AGORA2 pan-species DB into the next database release. Which organism are you missing right now, so I can check that it will be included.

[suetli19]

I've listed the species missing in the agora2 database (https://vmh.life/files/reconstructions/AGORA2/version2.01/mat_files/individual_reconstructions/) in this csv file with its taxa id.

Are there any other databases/resources where I can get these missing strains in their mat/xml file format so that I can include them to build the micom model?

absent_sp.csv

[suetli19]

Hi @cdiener,

I wonder if there are any updates regarding the missing organism in the database so that they can be included in the current model?

Thank you.