{
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"execution_count": 1,
"metadata": {
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"source": [
"from time import time\n",
"from random import Random\n",
"\n",
"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\n",
"\n",
"from cameo.flux_analysis.simulation import fba\n",
"import inspyred"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
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"outputs": [],
"source": [
"model = load_model(\"../tests/data/iJO1366.xml\")\n",
"of = biomass_product_coupled_yield(model.reactions.Ec_biomass_iJO1366_core_53p95M,\n",
" model.reactions.EX_succ_lp_e_rp_,\n",
" model.reactions.EX_glc_lp_e_rp_)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
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"outputs": [],
"source": [
"ko = ReactionKnockoutOptimization(model=model, objective_function=of, \n",
" simulation_method=fba, heuristic_method=inspyred.ec.GA)\n",
"ko.representation.remove(\"ATPM\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false,
"scrolled": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Starting optimization at Mon, 18 May 2015 00:11:31\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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