{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Predict expression modulation targets\n", "\n", "Cameo provides algorithms to search for genes or reactions that can be over or down regulated in order to achieve a given biological objective." ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": true }, "outputs": [], "source": [ "from cobra.io import read_sbml_model" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Load the E. coli core model." ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": true }, "outputs": [], "source": [ "model = read_sbml_model('data/e_coli_core.xml.gz')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Succinate production" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The production envelope looks like this." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "\n", "(function(global) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " var force = true;\n", "\n", " if (typeof (window._bokeh_onload_callbacks) === \"undefined\" || force === true) {\n", " window._bokeh_onload_callbacks = [];\n", " window._bokeh_is_loading = undefined;\n", " }\n", "\n", "\n", " \n", " if (typeof (window._bokeh_timeout) === \"undefined\" || force === true) {\n", " window._bokeh_timeout = Date.now() + 5000;\n", " window._bokeh_failed_load = false;\n", " }\n", "\n", " var NB_LOAD_WARNING = {'data': {'text/html':\n", " \"
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---|---|---|---|---|---|---|---|---|---|---|
ADK1 | \n", "0.0000 | \n", "0.0000 | \n", "0.0000 | \n", "-0.0000 | \n", "-0.0000 | \n", "-0.0000 | \n", "-0.0000 | \n", "-0.0000 | \n", "0.4103 | \n", "1.5273 | \n", "
ENO | \n", "15.2389 | \n", "15.7616 | \n", "16.2124 | \n", "16.5775 | \n", "16.9427 | \n", "17.3078 | \n", "17.7044 | \n", "18.6023 | \n", "19.2933 | \n", "19.6280 | \n", "
FBA | \n", "7.7569 | \n", "8.0365 | \n", "8.2425 | \n", "8.3610 | \n", "8.4796 | \n", "8.5981 | \n", "8.7478 | \n", "9.3931 | \n", "9.8308 | \n", "9.9109 | \n", "
FRD7 | \n", "0.0000 | \n", "0.0000 | \n", "0.0000 | \n", "1.4532 | \n", "3.1753 | \n", "4.8974 | \n", "6.5867 | \n", "7.7551 | \n", "9.1278 | \n", "10.8523 | \n", "
GAPD | \n", "16.4311 | \n", "16.8387 | \n", "17.1736 | \n", "17.4220 | \n", "17.6704 | \n", "17.9187 | \n", "18.1984 | \n", "18.9767 | \n", "19.5478 | \n", "19.7620 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
PPS | \n", "0.0000 | \n", "0.0000 | \n", "0.0000 | \n", "0.0000 | \n", "0.0000 | \n", "0.0000 | \n", "0.0000 | \n", "0.0000 | \n", "0.4103 | \n", "1.5273 | \n", "
SUCCt3 | \n", "1.4746 | \n", "2.9491 | \n", "4.4237 | \n", "5.8983 | \n", "7.3729 | \n", "8.8475 | \n", "10.3220 | \n", "11.7966 | \n", "13.2712 | \n", "14.7457 | \n", "
THD2 | \n", "0.0000 | \n", "0.0000 | \n", "0.0000 | \n", "0.0000 | \n", "0.0000 | \n", "0.0000 | \n", "0.1197 | \n", "2.1438 | \n", "2.9168 | \n", "1.5352 | \n", "
TPI | \n", "7.7569 | \n", "8.0365 | \n", "8.2425 | \n", "8.3610 | \n", "8.4796 | \n", "8.5981 | \n", "8.7478 | \n", "9.3931 | \n", "9.8308 | \n", "9.9109 | \n", "
EX_succ_e | \n", "1.4746 | \n", "2.9492 | \n", "4.4237 | \n", "5.8983 | \n", "7.3729 | \n", "8.8475 | \n", "10.3220 | \n", "11.7966 | \n", "13.2712 | \n", "14.7458 | \n", "
18 rows × 10 columns
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