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opencobra / cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.
http://opencobra.github.io/cobrapy/
GNU General Public License v2.0
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createMultipleSpeciesModel function can not find in cobrapy #1336

Closed wupeng1998 closed 1 year ago

wupeng1998 commented 1 year ago

Hi everyone, I want to simulate the interaction of bacterium like the method 2.7 of the article "https://pubmed.ncbi.nlm.nih.gov/36720400/", but I didn't find it in cobrapy createMultipleSpeciesModel function, how should I implement it in python?

cdiener commented 1 year ago

This is a function in the (Matlab-based) cobratoolbox not in cobrapy. You could look into MICOM if you want to run microbial community models on Python.

wupeng1998 commented 1 year ago

This is a function in the (Matlab-based) cobratoolbox not in cobrapy. You could look into MICOM if you want to run microbial community models on Python.

Ok, thank you. I know it's a function on matlab, but I'm getting errors when I replicate it to python, so I was wondering if anyone has ever replicated this function from MATLAB to Python,.

cdiener commented 1 year ago

The Community class in MICOM is somewhat similar, and the community objective is the same. So you could start there.

cdiener commented 1 year ago

Closing for now since it's not really a bug in cobrapy. Feel free to open a discussion topic. Best.