{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/joao/.virtualenvs/cameo-env/lib/python2.7/site-packages/IPython/parallel/client/client.py:452: RuntimeWarning: \n",
" Controller appears to be listening on localhost, but not on this machine.\n",
" If this is true, you should specify Client(...,sshserver='you@10.32.0.166')\n",
" or instruct your controller to listen on an external IP.\n",
" RuntimeWarning)\n",
"/Users/joao/.venvburrito/lib/python2.7/site-packages/setuptools-8.2-py2.7.egg/pkg_resources.py:2443: PEP440Warning: 'processing (0.52-pathos)' 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.\n",
"/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.\n",
"/Users/joao/.venvburrito/lib/python2.7/site-packages/setuptools-8.2-py2.7.egg/pkg_resources.py:2443: PEP440Warning: 'matlabengineforpython (R2014b)' 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.\n",
"/Users/joao/.venvburrito/lib/python2.7/site-packages/setuptools-8.2-py2.7.egg/pkg_resources.py:2443: PEP440Warning: 'pyre (0.8-pathos)' 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.\n"
]
}
],
"source": [
"from time import time\n",
"from random import Random\n",
"\n",
"from cameo.strain_design.heuristic import GeneKnockoutOptimization\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": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"model = load_model(\"/Users/joao/Documents/repos/cameo/tests/data/iJO1366.xml\")\n",
"of = biomass_product_coupled_yield(\"Ec_biomass_iJO1366_core_53p95M\", \"EX_succ_lp_e_rp_\", \"EX_glc_lp_e_rp_\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"ko = GeneKnockoutOptimization(model=model, objective_function=of, \n",
" simulation_method=fba, heuristic_method=inspyred.ec.GA)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Starting optimization at Tue, 14 Apr 2015 13:29:21\n"
]
},
{
"data": {
"text/html": [
" \n",
" \n",
" \n",
" \n",
" \n",
"
\n",
"
BokehJS successfully loaded.\n",
"