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In [2]:

    
import cameo
from cameo import load_model
from cameo.strain_design.heuristic import GeneKnockoutOptimization, ReactionKnockoutOptimization
from cameo.strain_design.heuristic.objective_functions import biomass_product_coupled_yield, product_yield, number_of_knockouts
from cameo.flux_analysis.simulation import fba
from cameo.parallel import SequentialView
import inspyred



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model = load_model("iMM904")



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objective1 = biomass_product_coupled_yield(model.reactions.biomass_SC5_notrace,
                                           model.reactions.EX_lac_D_e_,
                                           model.reactions.EX_glc_e_)

objective2 = number_of_knockouts()

objective = [objective1, objective2]



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ko = GeneKnockoutOptimization(model=model,
                              simulation_method=fba,
                              objective_function=objective,
                              heuristic_method=inspyred.ec.emo.NSGA2)



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results = ko.run(max_evaluations=3000, popuplation_size=100, view=SequentialView())









    



Starting optimization at Tue, 16 Jun 2015 14:42:09






    




    
        
        
        






    



Using saved session configuration for http://localhost:5006/
To override, pass 'load_from_config=False' to Session






    











    




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results



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