07-predict-heterologous-pathways.ipynb

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    "from IPython.display import display\n",
    "import re"
   ]
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   "cell_type": "markdown",
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   "source": [
    "# Predict heterologous pathways\n",
    "\n",
    "Predicting heterologous pathways is an important strategy to generate new viable strains. Because portfolio of available reactions is very large, computer assisted pathway design becomes essential. **Cameo** implements a pathway search algorithm using an universal biochemical reaction database that enumerates the shortest pathways."
   ]
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    "<div class=\"alert alert-warning\">\n",
    "If you're running this notebook on [try.cameo.bio](http://try.cameo.bio), things might run very slow due to our inability to provide access to the proprietary [CPLEX](https://www-01.ibm.com/software/commerce/optimization/cplex-optimizer/) solver on a public webserver. Furthermore, Jupyter kernels might crash and restart due to memory limitations on the server.\n",
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   "source": [
    "from cameo import models\n",
    "from cameo.strain_design import pathway_prediction"
   ]
  },
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    "model = models.bigg.iMM904"
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    "predictor = pathway_prediction.PathwayPredictor(model=model, compartment_regexp=re.compile(\".*_c$\"))"
   ]
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      "text/html": [
       "<span>Pathway 1</span>"
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       "<IPython.core.display.HTML object>"
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       "      <th>MNXR5336</th>\n",
       "      <td>vanillin + H2O + NAD(+) &lt;=&gt; NADH(2-) + 2.0 H(+...</td>\n",
       "      <td>-1000</td>\n",
       "      <td>1000</td>\n",
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       "    <tr>\n",
       "      <th>MNXR5340</th>\n",
       "      <td>formaldehyde + H2O + NAD(+) + 3,4-dihydroxyben...</td>\n",
       "      <td>-1000</td>\n",
       "      <td>1000</td>\n",
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       "    <tr>\n",
       "      <th>MNXR68718</th>\n",
       "      <td>H2O + 3,4-dihydroxybenzoate &lt;=&gt; 3-dehydroshiki...</td>\n",
       "      <td>-1000</td>\n",
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       "                                                    equation  lower_bound  \\\n",
       "MNXR5336   vanillin + H2O + NAD(+) <=> NADH(2-) + 2.0 H(+...        -1000   \n",
       "MNXR5340   formaldehyde + H2O + NAD(+) + 3,4-dihydroxyben...        -1000   \n",
       "MNXR68718  H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki...        -1000   \n",
       "\n",
       "           upper_bound  \n",
       "MNXR5336          1000  \n",
       "MNXR5340          1000  \n",
       "MNXR68718         1000  "
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       "      <th>MNXR230</th>\n",
       "      <td>NADP(+) + H2O + 3,4-dihydroxybenzoate &lt;=&gt; O2 +...</td>\n",
       "      <td>-1000</td>\n",
       "      <td>1000</td>\n",
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       "      <th>MNXR5336</th>\n",
       "      <td>vanillin + H2O + NAD(+) &lt;=&gt; NADH(2-) + 2.0 H(+...</td>\n",
       "      <td>-1000</td>\n",
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       "      <th>MNXR5340</th>\n",
       "      <td>formaldehyde + H2O + NAD(+) + 3,4-dihydroxyben...</td>\n",
       "      <td>-1000</td>\n",
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       "                                                   equation  lower_bound  \\\n",
       "MNXR230   NADP(+) + H2O + 3,4-dihydroxybenzoate <=> O2 +...        -1000   \n",
       "MNXR5336  vanillin + H2O + NAD(+) <=> NADH(2-) + 2.0 H(+...        -1000   \n",
       "MNXR5340  formaldehyde + H2O + NAD(+) + 3,4-dihydroxyben...        -1000   \n",
       "\n",
       "          upper_bound  \n",
       "MNXR230          1000  \n",
       "MNXR5336         1000  \n",
       "MNXR5340         1000  "
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       "<span>Pathway 3</span>"
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       "      <th>MNXR5336</th>\n",
       "      <td>vanillin + H2O + NAD(+) &lt;=&gt; NADH(2-) + 2.0 H(+...</td>\n",
       "      <td>-1000</td>\n",
       "      <td>1000</td>\n",
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       "      <th>MNXR5340</th>\n",
       "      <td>formaldehyde + H2O + NAD(+) + 3,4-dihydroxyben...</td>\n",
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       "      <td>H2O + 3,4-dihydroxybenzoate + NAD(+) &lt;=&gt; NADH(...</td>\n",
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       "                                                    equation  lower_bound  \\\n",
       "MNXR5336   vanillin + H2O + NAD(+) <=> NADH(2-) + 2.0 H(+...        -1000   \n",
       "MNXR5340   formaldehyde + H2O + NAD(+) + 3,4-dihydroxyben...        -1000   \n",
       "MNXR14769  H2O + 3,4-dihydroxybenzoate + NAD(+) <=> NADH(...        -1000   \n",
       "\n",
       "           upper_bound  \n",
       "MNXR5336          1000  \n",
       "MNXR5340          1000  \n",
       "MNXR14769         1000  "
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       "<span>Pathway 4</span>"
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       "      <th>MNXR5336</th>\n",
       "      <td>vanillin + H2O + NAD(+) &lt;=&gt; NADH(2-) + 2.0 H(+...</td>\n",
       "      <td>-1000</td>\n",
       "      <td>1000</td>\n",
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       "    <tr>\n",
       "      <th>MNXR5340</th>\n",
       "      <td>formaldehyde + H2O + NAD(+) + 3,4-dihydroxyben...</td>\n",
       "      <td>-1000</td>\n",
       "      <td>1000</td>\n",
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       "    <tr>\n",
       "      <th>MNXR6101</th>\n",
       "      <td>anthranilate + NADH(2-) + O2 + 3.0 H(+) &lt;=&gt; NH...</td>\n",
       "      <td>-1000</td>\n",
       "      <td>1000</td>\n",
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       "    <tr>\n",
       "      <th>MNXR7067</th>\n",
       "      <td>3,4-dihydroxybenzoate + H(+) &lt;=&gt; catechol + CO(2)</td>\n",
       "      <td>-1000</td>\n",
       "      <td>1000</td>\n",
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      "text/plain": [
       "                                                   equation  lower_bound  \\\n",
       "MNXR5336  vanillin + H2O + NAD(+) <=> NADH(2-) + 2.0 H(+...        -1000   \n",
       "MNXR5340  formaldehyde + H2O + NAD(+) + 3,4-dihydroxyben...        -1000   \n",
       "MNXR6101  anthranilate + NADH(2-) + O2 + 3.0 H(+) <=> NH...        -1000   \n",
       "MNXR7067  3,4-dihydroxybenzoate + H(+) <=> catechol + CO(2)        -1000   \n",
       "\n",
       "          upper_bound  \n",
       "MNXR5336         1000  \n",
       "MNXR5340         1000  \n",
       "MNXR6101         1000  \n",
       "MNXR7067         1000  "
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   "source": [
    "pathways = predictor.run(product=\"vanillin\", max_predictions=4)"
   ]
  },
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       "                <td><strong>Id</strong></td><td>MNXR5336</td>\n",
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       "            <tr>\n",
       "                <td><strong>Name</strong></td><td>rhea:13309</td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                <td><strong>Stoichiometry</strong></td><td>MNXM754 + MNXM2 + MNXM8 <=> MNXM10 + 2.0 MNXM1 + MNXM982</td>\n",
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       "            <tr>\n",
       "                <td><strong>Lower bound</strong></td><td>-1000.000000</td>\n",
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       "<Reaction MNXR5336 at 0x11eb66780>"
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       "            Bokeh.embed.embed_items(docs_json, render_items);\n",
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       "        inline_js[i](window.Bokeh);\n",
       "      }\n",
       "    }\n",
       "  \n",
       "    if (window._bokeh_is_loading === 0) {\n",
       "      console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
       "      run_inline_js();\n",
       "    } else {\n",
       "      load_libs(js_urls, function() {\n",
       "        console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n",
       "        run_inline_js();\n",
       "      });\n",
       "    }\n",
       "  }(this));\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "pathways.plot_production_envelopes(model, objective=model.reactions.BIOMASS_SC5_notrace)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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