Converting excel file to a sbml for community models

I am trying to use community model for elasticities in MICOM. My taxonomy file is an excel file that has the id information, reaction and metabolite number and abundance data (same as the one I used for build and grow functions). As far as I understood I have to use a sbml file with .xml extension. I have checked the forum and previous replies about this topic but I still didn't understand it.
Thanks for your interest!!

Hi @dgenc, sorry for the late replay. I haven't updated my E-mail in the forum yet.

So the taxonomy file in MICOM shows you how much of each taxon is there and than you have a separate database with a model for each taxon (which are built from SBML) like the ones provided here. For the Qiime interface you need your inputs to be prior Qiime artifacts (a feature table and a taxon table). However, you could use the Python interface to build the community models (just need to read your table with pandas).

You can also follow our free online courses. For instance Day 2 from 2022 might fit. Here the difference would be that you taxonomy table comes from your excel and not previous Qiime2 commands.


hello @cdiener! thanks for your reply!
when I tried to run the community models I created via python for the elasticities, I got zero elasticities for my exchanges.
I'll also take a look at the videos at the link!
Thanks again!