Simulations of E. coli

#Simulations-of-

This notebook contains simple tests of the E. coli model iML1515 both in regular and ecModel format.

Benjamín J. Sánchez, 2019-10-15

1. Loading models

#1.-Loading-models

(temporal, eventually they will be available in the master branch)

2. Simulating models

#2.-Simulating-models

2.1. Simulating the metabolic model

#2.1.-Simulating-the-metabolic-model
Loading output library...
Loading output library...
Loading output library...

Note that in total 16 metabolites are consumed: oxygen, glucose, ammonia, phosphate, sulphate and 11 minerals.

2.2. Simulating the enzyme-constrained model as-is

#2.2.-Simulating-the-enzyme-constrained-model-
Loading output library...

2.3 Fixing the enzyme-constrained model

#2.3-Fixing-the-enzyme-constrained-model

cobrapy cannot handle upper bounds = Inf, therefore we need to replace them with 1000 (standard in the field):

Loading output library...

Pretty high objective function -> we need to lower the upper bound of glucose uptake:

Loading output library...

Nothing changed -> let's look at the summary of in/out fluxes:

Loading output library...

We see that there are many uptake fluxes fully unconstrained. Let's fix all of them to zero except for the original 16:

Loading output library...

Success!!

3. Model export and cleanup

#3.-Model-export-and-cleanup

4. Changing GAM

#4.-Changing-GAM