Same individual growth rates

[lhtxa]

Hi! Is there a way to find a solution where some, or all, individual growth rates have the same value?

[cdiener]

Definitely possible but currently a bit clunky. Cooperative Tradeoff will push the solution towards that by default, especially if you choose a low tradeoff. But it is also possible to enforce the same growth rates directly by adding ratio constraints. Here is an example:

import micom as mm

com = mm.Community(mm.data.test_taxonomy())
constraints = []
ref_taxon_objective = com.constraints["objective_" + com.taxa[0]].expression
for tax in com.taxa[1:]:
    c = com.problem.Constraint(
        com.constraints["objective_" + tax].expression - ref_taxon_objective,
        name="ratio_" + tax,
        lb=0, ub=0
    )
    constraints.append(c)
with com:
    com.add_cons_vars(constraints)
    sol = com.optimize()   # maximizes community growth with the constraints applied

print(sol.members)

Which will give:

                    abundance  growth_rate  reactions  metabolites
compartments                                                      
Escherichia_coli_1       0.25     0.873922         95           72
Escherichia_coli_2       0.25     0.873922         95           72
Escherichia_coli_3       0.25     0.873922         95           72
Escherichia_coli_4       0.25     0.873922         95           72
medium                    NaN          NaN         20           20

So this is planned to be implemented as a helper function already.

[lhtxa]

Thanks for the reply with the code!
Are the results expected to be the same whatever is the member defined as ref_taxon? I varied it and did get the same results.

[cdiener]

Yes, reference taxon does not matter.