Setting protein concentration in ec-yeast

[cplong90]

Hi @carrascomj, minor issue and question on setting experimental protein concentrations in the yeast model.

• Small issue: experimental.limit_proteins() fails to find the correct reaction in the ecyeast8 model. It assumes a format of f"prot_{protein_id}" where in the yeast model (unlike E. coli) it contains the compartment, e.g. f"prot_{protein_id}[c]". What do you think of relying on the df_prot for the uniprot to reaction mapping?
• More general behavior question -- what is the difference in setting protein.concentration vs. protein.upper_bound ? Intuitively I would expect the former to fix the abundance, while the latter sets a maximum abundance. I'm noticing that when I explicitly set a concentration for a production enzyme and then optimize with a biomass objective, the protein has apparently 0 abundance in the solution. It's very possible I'm doing something incorrectly but thought I'd check in on the expected behavior.

[carrascomj]

Regarding the first point, someone reported that on my group last month. I believe the solution would be to take the identifiers from the dataframe as you describe and assume nothing about them.

I will give a check to the second point. I don't remember the exact logic, but I think concentration and upper_bound where supposed to be the same thing in the case of proteins.

[carrascomj]

I have checked the concentration and the upper_bound.

The design was that the user was not supposed to interact with upper_bound, but use add_concentration instead. .upper_bound is still there in case the user wants to have a constraint in a protein that it is not a concentration for whatever reason.

.concentration is effectively the .upper_bound. The only difference is that, concentration is aware of the common protein pool, so it will update everything properly.