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segrelab / cometspy

Python interface for running COMETS simulations and analyzing the results
GNU General Public License v3.0
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Growth rate after setting media concentration and parame #17

Open behzadk opened 2 years ago

behzadk commented 2 years ago

Hi all,

Is there a function like model.slim_optimize() that can be used on a cometspy model?

I would like to be able to get the growth rate after setting the environment concentrations and Michaelis menten parameters. I could do a short simulation and infer from that, but if I could get the growth rate directly that would be preferable!

Thanks, Behzad

jeremymchacon commented 2 years ago

Hi,

COMETS doesn't have a function to do that, but if you are using the same solver in cobrapy as well as in COMETS (e.g. gurobi), then setting up the cobra model with the right media and doing slim_optimize() should be the same.

You'll want to set the lower bounds in your cobra exchanges to be vmax * x / (x + km), where vmax and km are the MM parameters you chose, and x is the concentration (i.e. mmol added divided by the spaceWidth cubed).