In [1]:

    

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


    

In [4]:

    

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_)


    

In [5]:

    

ko = ReactionKnockoutOptimization(model=model, objective_function=of, 
                                  simulation_method=fba, heuristic_method=inspyred.ec.GA)
ko.representation.remove("ATPM")


    

In [ ]:

    

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






    












    





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