search

opencobra / cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.
http://opencobra.github.io/cobrapy/
GNU General Public License v2.0
467 stars 218 forks source link

minimal media growth rate #1307

Closed amarsh26 closed 1 year ago

amarsh26 commented 1 year ago

Hello,

The documentation for minimal media provides the following example.

`from cobra.medium import minimal_medium

max_growth = model.slim_optimize() minimal_medium(model, max_growth)`

When I execute this code on the iML1515 model of E. coli, I receive the following results.

0.8769972144269745 (growth rate from using the minimal media function) 0.8769972144269719 (growth rate with the default)

While this is a very slight difference, I was wondering to what level of precision do you expect the growth rate to match between the default configuration and the growth rate using minimal media.

Thanks for your help.

cdiener commented 1 year ago

The tolerance of the numerical solver can be inspected with model.tolerance. This is the largest relative and absolute deviation that should be expected. I think by default it somewhere between 1e-6 and 1e-9 so the deviation is within that. You can also adjust this tolerance by setting it to something smaller but it will increase computation time.

amarsh26 commented 1 year ago

Thanks so much for your help!