search

segrelab / comets

Computation of Microbial Ecosystems in Time and Space
19 stars 10 forks source link

Fluxes variation analysis/optimization #47

Closed zorzansi closed 4 months ago

zorzansi commented 9 months ago

Hi, we are working on a project involving a microbial community, and we would like to find an optimal flux which remains feasible but maximizes a metabolite or a metabolite(s) class. Do you think that this can be implemented in Comets and how many CPU and RAM do you think such an optimization might require for a community of 6-12 species?

Thank you!

dukovski commented 9 months ago

Hi, Thanks for the interest. Yes, you can do that in comets. I am not sure what you mean by maximizes a metabolite. If you mean maximum production of a secreted metabolite, yes you can explore that by changing the exchange parameters and/or setting objective reactions that include the exchange reaction for the metabolite. In Comets, you can set the objective to be different than the biomass.

For 6-12 species, in well mixed conditions (single spatial grid point) you can do it in practically any computer, including a laptop. If you do it in spatially structured environment, it takes few days to run 10000 steps for two models in 400x400 grid, running 8 threads in parallel. So you can easily do 6-12 species, if you run 100x100 spatial grid for 1000 time points, for example.

I hope this helps.

Ilija

dukovski commented 4 months ago

I am closing this.