from time import time
from random import Random
from cameo.strain_design.heuristic import ReactionKnockoutOptimization
from cameo import load_model
from cameo.strain_design.heuristic.objective_functions import biomass_product_coupled_yield
from cameo.flux_analysis.simulation import fba
import inspyred
model = load_model("../tests/data/iJO1366.xml")
of = biomass_product_coupled_yield(model.reactions.Ec_biomass_iJO1366_core_53p95M,
model.reactions.EX_succ_lp_e_rp_,
model.reactions.EX_glc_lp_e_rp_)
ko = ReactionKnockoutOptimization(model=model, objective_function=of,
simulation_method=fba, heuristic_method=inspyred.ec.GA)
ko.representation.remove("ATPM")
ko.run(max_evaluations=30000, n=1, mutation_rate=0.15, indel_rate=0.185)
Starting optimization at Mon, 18 May 2015 00:11:31
Using saved session configuration for http://localhost:5006/ To override, pass 'load_from_config=False' to Session