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"source": [
"from cameo.strain_design.heuristic import ReactionKnockoutOptimization\n",
"from cameo import load_model\n",
"from cameo.strain_design.heuristic.objective_functions import biomass_product_coupled_yield, product_yield, number_of_knockouts\n",
"from cameo.flux_analysis.simulation import fba\n",
"import cameo\n",
"import inspyred"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"model = load_model(\"../tests/data/iJO1366.xml\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
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"source": [
"of1 = product_yield(model.reactions.EX_ac_lp_e_rp_.id, model.reactions.EX_glc_lp_e_rp_.id)\n",
"of2 = number_of_knockouts()\n",
"of3 = biomass_product_coupled_yield(model.reactions.Ec_biomass_iJO1366_core_53p95M.id,\n",
" model.reactions.EX_ac_lp_e_rp_.id,\n",
" model.reactions.EX_glc_lp_e_rp_.id)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
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"source": [
"ko = ReactionKnockoutOptimization(model=model, objective_function=[of1, of2],\n",
" simulation_method=fba, heuristic_method=inspyred.ec.emo.NSGA2)"
]
},
{
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"execution_count": null,
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"output_type": "stream",
"text": [
"Starting optimization at Mon, 18 May 2015 00:08:14\n"
]
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"Using saved session configuration for http://localhost:5006/\n",
"To override, pass 'load_from_config=False' to Session\n"
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