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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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SteadyCom on CarveMe models #85

Closed arianccbasile closed 4 years ago

arianccbasile commented 4 years ago

Dear Daniel, have you ever tried to run the SteadyCom pipeline (https://opencobra.github.io/cobratoolbox/stable/modules/analysis/multiSpecies/SteadyCom/index.html) with models created by CarveMe? I am trying but I get a weird error: in the simulation, it always results that only one of the members of the community has a growth rate different than 0. Any idea on how to manage?

Sincerely, Arianna Basile

cdanielmachado commented 4 years ago

Hi Arianna,

I have not tried with the cobratoolbox implementation, but I also wrote a python implementation of SteadyCom in reframed, which I have used with CarveMe models:

https://github.com/cdanielmachado/reframed/blob/master/reframed/community/SteadyCom.py

If there are no obligatory cross-feeding interactions, it is normal that only one of the species will grow. This is a limitation of SteadyCom itself. Since it maximizes community growth, a community with only the fastest-growing species is the optimal solution.

arianccbasile commented 4 years ago

Thank you very much, Daniel. Actually so far I have never tried your reframed. I have now the occasion to try. :)