This notebook contains simple tests of the E. coli model
iML1515 both in regular and ecModel format.
Benjamín J. Sánchez, 2019-10-15
(temporal, eventually they will be available in the master branch)
Note that in total 16 metabolites are consumed: oxygen, glucose, ammonia, phosphate, sulphate and 11 minerals.
cobrapy cannot handle upper bounds =
Inf, therefore we need to replace them with
1000 (standard in the field):
Pretty high objective function -> we need to lower the upper bound of glucose uptake:
Nothing changed -> let's look at the summary of in/out fluxes:
We see that there are many uptake fluxes fully unconstrained. Let's fix all of them to zero except for the original 16: