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.