1.4 Converting Gene or Reaction Knockouts into Metabolite Knockouts

from marsi.cobra.strain_design.post_processing import replace_strain_design_results

from cameo import models
from cameo.strain_design import OptGene
from cameo.util import TimeMachine
from pandas import DataFrame

Design a D-lactate producing strain

In this example we are going to create strain designs using OptGene.

Model	Medium	Aerobicity	Target
iJO1366	Glucose	Anaerobic	lac__D_e

model = models.bigg.iJO1366

model.reactions.EX_o2_e.lower_bound = 0

We search for reactions, because they can be directly translated into metabolite targets

optgene = OptGene(model, manipulation_type="reactions", essential_reactions=["ATPM"])

results = optgene.run(target="EX_lac__D_e",
                      biomass="BIOMASS_Ec_iJO1366_core_53p95M",
                      substrate="EX_glc__D_e",
                      max_knockouts=15,
                      max_evaluations=15000)

df = results.data_frame

df

replacements = replace_strain_design_results(model, results, results._objective_function,
                                             results._simulation_method, results._simulation_kwargs)

replacements.style