In [1]:

    

from cameo import load_model
from cameo.strain_design.heuristic.multiprocess import MultiprocessReactionKnockoutOptimization
from cameo.strain_design.heuristic.objective_functions import biomass_product_coupled_yield
from cameo.flux_analysis.simulation import fba
import inspyred


    

    




/Users/joao/.virtualenvs/cameo-env/lib/python2.7/site-packages/IPython/parallel/client/client.py:452: RuntimeWarning: 
            Controller appears to be listening on localhost, but not on this machine.
            If this is true, you should specify Client(...,sshserver='you@10.32.0.166')
            or instruct your controller to listen on an external IP.
  RuntimeWarning)
/Users/joao/.venvburrito/lib/python2.7/site-packages/setuptools-8.2-py2.7.egg/pkg_resources.py:2443: PEP440Warning: 'cameo (v0.2.0-51-gd721048-dirty)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions.

In [2]:

    

model = load_model("../tests/data/iJO1366.xml")


    

In [3]:

    

of = biomass_product_coupled_yield("Ec_biomass_iJO1366_core_53p95M", "EX_ac_lp_e_rp_", "EX_glc_lp_e_rp_")


    

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mp = MultiprocessReactionKnockoutOptimization(model=model, heuristic_method=inspyred.ec.GA,
                                              objective_function=of, simulation_method=fba)


    

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from cameo import parallel
mp.run(max_evaluations=300, n=2, view=parallel.MultiprocessingView())


    

    




Start IPython Notebook Multiprocess Progress Observer






    





    
        
        
        
    

        
        BokehJS successfully loaded.
    






    




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






    












    




Start IPython Notebook Bokeh Multiprocess Plot Observer

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