{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Getting started with cameo "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**cameo** reuses and extends model data structures defined by [cobrapy](https://opencobra.github.io/cobrapy/) (**CO**nstraints-**B**ased **R**econstruction and **A**nalysis tool for **Py**thon). So, in addition to following this quick start guide and other **cameo** tutorials, we encourage you to explore cobrapy's [documentation](https://cobrapy.readthedocs.org/en/latest/cobra.core.html) as well."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Step 1: Load a model\n",
    "-------------------\n",
    "\n",
    "Loading a model is easy. Just import the `~cameo.io.load_model` function."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cameo import load_model"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For example, load a genome-scale metabolic reconstruction of _Escherichia coli_."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "model = load_model(\"iJO1366\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Models, reactions, metabolites, etc., return HTML when evaluated in Jupyter notebooks and can be easily inspected."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <table>\n",
       "            <tr>\n",
       "                <td><strong>Name</strong></td>\n",
       "                <td>iJO1366</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Memory address</strong></td>\n",
       "                <td>0x01120756d8</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of metabolites</strong></td>\n",
       "                <td>1805</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Number of reactions</strong></td>\n",
       "                <td>2583</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Objective expression</strong></td>\n",
       "                <td>-1.0*BIOMASS_Ec_iJO1366_core_53p95M_reverse_5c8b1 + 1.0*BIOMASS_Ec_iJO1366_core_53p95M</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Compartments</strong></td>\n",
       "                <td>extracellular space, cytosol, periplasm</td>\n",
       "            </tr>\n",
       "          </table>"
      ],
      "text/plain": [
       "<Model iJO1366 at 0x1120756d8>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 2: Simulate a model\n",
    "\n",
    "The model can be simulated by executing `optimize`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "solution = model.optimize()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "A quick overview of the solution can be obtained in inspecting it."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<strong><em>Optimal</em> solution with objective value 0.982</strong><br><div>\n",
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       "  </tbody>\n",
       "</table>\n",
       "<p>2583 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "<Solution 0.982 at 0x115a61ba8>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "solution"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "A data frame representation of the solution is accessible via `solution.to_frame()`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
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       "2AGPA180tipp   0.000000   0.000000e+00\n",
       "...                 ...            ...\n",
       "VALTRS         0.000000   0.000000e+00\n",
       "VALabcpp       0.000000  -6.221481e-03\n",
       "VALt2rpp       0.000000   0.000000e+00\n",
       "VALtex         0.000000   0.000000e+00\n",
       "VPAMTr         0.000000   0.000000e+00\n",
       "WCOS           0.000000   0.000000e+00\n",
       "X5PL3E         0.000000   0.000000e+00\n",
       "XAND           0.000000   0.000000e+00\n",
       "XANt2pp        0.000000  -2.073827e-03\n",
       "XANtex         0.000000   0.000000e+00\n",
       "XANtpp         0.000000   0.000000e+00\n",
       "XMPtex         0.000000   0.000000e+00\n",
       "XPPT           0.000000   0.000000e+00\n",
       "XTSNH          0.000000  -8.295308e-03\n",
       "XTSNt2rpp      0.000000   0.000000e+00\n",
       "XTSNtex        0.000000   0.000000e+00\n",
       "XYLI1          0.000000   0.000000e+00\n",
       "XYLI2          0.000000   0.000000e+00\n",
       "XYLK           0.000000  -1.387779e-17\n",
       "XYLK2          0.000000  -1.387779e-17\n",
       "XYLUt2pp       0.000000   0.000000e+00\n",
       "XYLUtex        0.000000   0.000000e+00\n",
       "XYLabcpp       0.000000  -6.221481e-03\n",
       "XYLt2pp        0.000000   0.000000e+00\n",
       "XYLtex         0.000000   0.000000e+00\n",
       "ZN2abcpp       0.000000  -8.295308e-03\n",
       "ZN2t3pp        0.000000  -2.073827e-03\n",
       "ZN2tpp         0.000335   0.000000e+00\n",
       "ZNabcpp        0.000000  -8.295308e-03\n",
       "Zn2tex         0.000335  -0.000000e+00\n",
       "\n",
       "[2583 rows x 2 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "solution.to_frame()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Data frames make it very easy to process results. For example, let's take a look at reactions with flux != 0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>fluxes</th>\n",
       "      <th>reduced_costs</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>3OAR140</th>\n",
       "      <td>0.076452</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3OAS140</th>\n",
       "      <td>0.076452</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5DOAN</th>\n",
       "      <td>0.000221</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>A5PISO</th>\n",
       "      <td>0.038226</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AACPS3</th>\n",
       "      <td>0.125378</td>\n",
       "      <td>-1.387779e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AACPS4</th>\n",
       "      <td>0.147776</td>\n",
       "      <td>-2.775558e-17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AACPS7</th>\n",
       "      <td>0.076452</td>\n",
       "      <td>-2.775558e-17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACACT1r</th>\n",
       "      <td>0.349606</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACACT2r</th>\n",
       "      <td>0.349606</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACACT3r</th>\n",
       "      <td>0.349606</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACACT4r</th>\n",
       "      <td>0.349606</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACACT5r</th>\n",
       "      <td>0.349606</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACACT6r</th>\n",
       "      <td>0.273154</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACACT7r</th>\n",
       "      <td>0.273154</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACCOAC</th>\n",
       "      <td>0.076458</td>\n",
       "      <td>-7.090682e-17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACGK</th>\n",
       "      <td>0.290578</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACGS</th>\n",
       "      <td>0.290578</td>\n",
       "      <td>2.927346e-17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACHBS</th>\n",
       "      <td>0.285408</td>\n",
       "      <td>-6.938894e-18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACLS</th>\n",
       "      <td>0.858857</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACOAD1f</th>\n",
       "      <td>-0.349606</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACOAD2f</th>\n",
       "      <td>-0.349606</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACOAD3f</th>\n",
       "      <td>-0.349606</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACOAD4f</th>\n",
       "      <td>-0.349606</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACOAD5f</th>\n",
       "      <td>-0.349606</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACOAD6f</th>\n",
       "      <td>-0.273154</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACOAD7f</th>\n",
       "      <td>-0.125378</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACODA</th>\n",
       "      <td>0.290578</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACONTa</th>\n",
       "      <td>4.857777</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACONTb</th>\n",
       "      <td>4.857777</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACOTA</th>\n",
       "      <td>-0.290578</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TMDS</th>\n",
       "      <td>0.025705</td>\n",
       "      <td>-5.551115e-17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TMPK</th>\n",
       "      <td>0.000219</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TMPPP</th>\n",
       "      <td>0.000219</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TPI</th>\n",
       "      <td>7.645371</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TRDR</th>\n",
       "      <td>0.243502</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TRPAS2</th>\n",
       "      <td>-0.055841</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TRPS3</th>\n",
       "      <td>0.055841</td>\n",
       "      <td>2.775558e-17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TYRL</th>\n",
       "      <td>0.000219</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TYRTA</th>\n",
       "      <td>-0.135684</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>U23GAAT</th>\n",
       "      <td>0.038226</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UAAGDS</th>\n",
       "      <td>0.027298</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UAGAAT</th>\n",
       "      <td>0.038226</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UAGCVT</th>\n",
       "      <td>0.027298</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UAGDP</th>\n",
       "      <td>0.092822</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UAGPT3</th>\n",
       "      <td>0.027298</td>\n",
       "      <td>-5.551115e-17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UAMAGS</th>\n",
       "      <td>0.027298</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UAMAS</th>\n",
       "      <td>0.027298</td>\n",
       "      <td>5.551115e-17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UAPGR</th>\n",
       "      <td>0.027298</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UDCPDP</th>\n",
       "      <td>0.027298</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UDCPDPS</th>\n",
       "      <td>0.000054</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UGMDDS</th>\n",
       "      <td>0.027298</td>\n",
       "      <td>1.110223e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UHGADA</th>\n",
       "      <td>0.038226</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UMPK</th>\n",
       "      <td>0.371375</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UPP3MT</th>\n",
       "      <td>0.000219</td>\n",
       "      <td>1.110223e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UPP3S</th>\n",
       "      <td>0.000438</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UPPDC1</th>\n",
       "      <td>0.000219</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>USHD</th>\n",
       "      <td>0.019113</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>VALTA</th>\n",
       "      <td>-0.415702</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ZN2tpp</th>\n",
       "      <td>0.000335</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Zn2tex</th>\n",
       "      <td>0.000335</td>\n",
       "      <td>-0.000000e+00</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>436 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "           fluxes  reduced_costs\n",
       "3OAR140  0.076452   0.000000e+00\n",
       "3OAS140  0.076452   0.000000e+00\n",
       "5DOAN    0.000221   0.000000e+00\n",
       "A5PISO   0.038226   0.000000e+00\n",
       "AACPS3   0.125378  -1.387779e-16\n",
       "AACPS4   0.147776  -2.775558e-17\n",
       "AACPS7   0.076452  -2.775558e-17\n",
       "ACACT1r  0.349606   0.000000e+00\n",
       "ACACT2r  0.349606   0.000000e+00\n",
       "ACACT3r  0.349606   0.000000e+00\n",
       "ACACT4r  0.349606   0.000000e+00\n",
       "ACACT5r  0.349606   0.000000e+00\n",
       "ACACT6r  0.273154   0.000000e+00\n",
       "ACACT7r  0.273154   0.000000e+00\n",
       "ACCOAC   0.076458  -7.090682e-17\n",
       "ACGK     0.290578   0.000000e+00\n",
       "ACGS     0.290578   2.927346e-17\n",
       "ACHBS    0.285408  -6.938894e-18\n",
       "ACLS     0.858857   0.000000e+00\n",
       "ACOAD1f -0.349606   0.000000e+00\n",
       "ACOAD2f -0.349606   0.000000e+00\n",
       "ACOAD3f -0.349606   0.000000e+00\n",
       "ACOAD4f -0.349606   0.000000e+00\n",
       "ACOAD5f -0.349606   0.000000e+00\n",
       "ACOAD6f -0.273154   0.000000e+00\n",
       "ACOAD7f -0.125378   0.000000e+00\n",
       "ACODA    0.290578   0.000000e+00\n",
       "ACONTa   4.857777   0.000000e+00\n",
       "ACONTb   4.857777   0.000000e+00\n",
       "ACOTA   -0.290578   0.000000e+00\n",
       "...           ...            ...\n",
       "TMDS     0.025705  -5.551115e-17\n",
       "TMPK     0.000219   0.000000e+00\n",
       "TMPPP    0.000219   0.000000e+00\n",
       "TPI      7.645371   0.000000e+00\n",
       "TRDR     0.243502   0.000000e+00\n",
       "TRPAS2  -0.055841   0.000000e+00\n",
       "TRPS3    0.055841   2.775558e-17\n",
       "TYRL     0.000219   0.000000e+00\n",
       "TYRTA   -0.135684   0.000000e+00\n",
       "U23GAAT  0.038226   0.000000e+00\n",
       "UAAGDS   0.027298   0.000000e+00\n",
       "UAGAAT   0.038226   0.000000e+00\n",
       "UAGCVT   0.027298   0.000000e+00\n",
       "UAGDP    0.092822   0.000000e+00\n",
       "UAGPT3   0.027298  -5.551115e-17\n",
       "UAMAGS   0.027298   0.000000e+00\n",
       "UAMAS    0.027298   5.551115e-17\n",
       "UAPGR    0.027298   0.000000e+00\n",
       "UDCPDP   0.027298   0.000000e+00\n",
       "UDCPDPS  0.000054   0.000000e+00\n",
       "UGMDDS   0.027298   1.110223e-16\n",
       "UHGADA   0.038226   0.000000e+00\n",
       "UMPK     0.371375   0.000000e+00\n",
       "UPP3MT   0.000219   1.110223e-16\n",
       "UPP3S    0.000438   0.000000e+00\n",
       "UPPDC1   0.000219   0.000000e+00\n",
       "USHD     0.019113   0.000000e+00\n",
       "VALTA   -0.415702   0.000000e+00\n",
       "ZN2tpp   0.000335   0.000000e+00\n",
       "Zn2tex   0.000335  -0.000000e+00\n",
       "\n",
       "[436 rows x 2 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "solution.to_frame().query('fluxes != 0')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 3: Exploring a model\n",
    "\n",
    "Objects—models, reactions, metabolites, genes—can easily be explored in the Jupyter notebook, taking advantage of tab completion. For example, place your cursor after the period in `model.reactions.` and press the TAB key. A dialog will appear that allows you to navigate the list of reactions encoded in the model. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <table>\n",
       "            <tr>\n",
       "                <td><strong>Reaction identifier</strong></td><td>PGK</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Name</strong></td><td>Phosphoglycerate kinase</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Memory address</strong></td>\n",
       "                <td>0x01129829b0</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Stoichiometry</strong></td>\n",
       "                <td>\n",
       "                    <p style='text-align:right'>3pg_c + atp_c <=> 13dpg_c + adp_c</p>\n",
       "                    <p style='text-align:right'>3-Phospho-D-glycerate + ATP C10H12N5O13P3 <=> 3-Phospho-D-glyceroyl phosphate + ADP C10H12N5O10P2</p>\n",
       "                </td>\n",
       "            </tr><tr>\n",
       "                <td><strong>GPR</strong></td><td>b2926</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Lower bound</strong></td><td>-1000.0</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Upper bound</strong></td><td>1000.0</td>\n",
       "            </tr>\n",
       "        </table>\n",
       "        "
      ],
      "text/plain": [
       "<Reaction PGK at 0x1129829b0>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model.reactions.PGK # delete PGK, place your cursor after the period and press the TAB key."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For example, you can access the E4PD (_Erythrose 4-phosphate dehydrogenase_) reaction in the model."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <table>\n",
       "            <tr>\n",
       "                <td><strong>Reaction identifier</strong></td><td>E4PD</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Name</strong></td><td>Erythrose 4-phosphate dehydrogenase</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Memory address</strong></td>\n",
       "                <td>0x0112606160</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Stoichiometry</strong></td>\n",
       "                <td>\n",
       "                    <p style='text-align:right'>e4p_c + h2o_c + nad_c <=> 4per_c + 2.0 h_c + nadh_c</p>\n",
       "                    <p style='text-align:right'>D-Erythrose 4-phosphate + H2O H2O + Nicotinamide adenine dinucleotide <=> 4-Phospho-D-erythronate + 2.0 H+ + Nicotinamide adenine dinucleotide - reduced</p>\n",
       "                </td>\n",
       "            </tr><tr>\n",
       "                <td><strong>GPR</strong></td><td>b2927 or b1779</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Lower bound</strong></td><td>-1000.0</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Upper bound</strong></td><td>1000.0</td>\n",
       "            </tr>\n",
       "        </table>\n",
       "        "
      ],
      "text/plain": [
       "<Reaction E4PD at 0x112606160>"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model.reactions.E4PD"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Be aware that, due to variable naming restrictions in Python, dot notation access to reactions (and other objects) might not work in some cases."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "# model.reactions.12DGR120tipp  # uncommenting and running this cell will produce a syntax error"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "In those cases you need to use the `model.reactions.get_by_id`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <table>\n",
       "            <tr>\n",
       "                <td><strong>Reaction identifier</strong></td><td>12DGR120tipp</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Name</strong></td><td>1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C12:0)</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Memory address</strong></td>\n",
       "                <td>0x0112506ba8</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Stoichiometry</strong></td>\n",
       "                <td>\n",
       "                    <p style='text-align:right'>12dgr120_p --> 12dgr120_c</p>\n",
       "                    <p style='text-align:right'>1,2-Diacyl-sn-glycerol (didodecanoyl, n-C12:0) --> 1,2-Diacyl-sn-glycerol (didodecanoyl, n-C12:0)</p>\n",
       "                </td>\n",
       "            </tr><tr>\n",
       "                <td><strong>GPR</strong></td><td></td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Lower bound</strong></td><td>0.0</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Upper bound</strong></td><td>1000.0</td>\n",
       "            </tr>\n",
       "        </table>\n",
       "        "
      ],
      "text/plain": [
       "<Reaction 12DGR120tipp at 0x112506ba8>"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model.reactions.get_by_id('12DGR120tipp')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Metabolites are accessible through `model.metabolites`. For example, D-glucose in the cytosol compartment."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <table>\n",
       "            <tr>\n",
       "                <td><strong>Metabolite identifier</strong></td><td>glc__D_c</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Name</strong></td><td>D-Glucose</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Memory address</strong></td>\n",
       "                <td>0x01120db4a8</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Formula</strong></td><td>C6H12O6</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>Compartment</strong></td><td>c</td>\n",
       "            </tr><tr>\n",
       "                <td><strong>In 19 reaction(s)</strong></td><td>\n",
       "                    GLCt2pp, GLCATr, TRE6PH, MLTG2, G6PP, LACZ, MLTG3, AMALT1, HEX1, XYLI2, MLTG4, GALS3, GLCabcpp, AMALT2, MLTG5, AMALT3, AMALT4, TREH, MLTG1</td>\n",
       "            </tr>\n",
       "        </table>"
      ],
      "text/plain": [
       "<Metabolite glc__D_c at 0x1120db4a8>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model.metabolites.glc__D_c"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And it is easy to find the associated reactions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "frozenset({<Reaction AMALT1 at 0x11257a978>,\n",
       "           <Reaction AMALT2 at 0x11257aa58>,\n",
       "           <Reaction AMALT3 at 0x11257aa90>,\n",
       "           <Reaction AMALT4 at 0x11257ab00>,\n",
       "           <Reaction G6PP at 0x112671940>,\n",
       "           <Reaction GALS3 at 0x112679630>,\n",
       "           <Reaction GLCATr at 0x1126864e0>,\n",
       "           <Reaction GLCabcpp at 0x11268d240>,\n",
       "           <Reaction GLCt2pp at 0x11268d438>,\n",
       "           <Reaction HEX1 at 0x1126bf588>,\n",
       "           <Reaction LACZ at 0x1126e2940>,\n",
       "           <Reaction MLTG1 at 0x1129253c8>,\n",
       "           <Reaction MLTG2 at 0x112925518>,\n",
       "           <Reaction MLTG3 at 0x112925550>,\n",
       "           <Reaction MLTG4 at 0x1129255c0>,\n",
       "           <Reaction MLTG5 at 0x112925630>,\n",
       "           <Reaction TRE6PH at 0x112a0b4e0>,\n",
       "           <Reaction TREH at 0x112a0b748>,\n",
       "           <Reaction XYLI2 at 0x112a30940>})"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model.metabolites.glc__D_c.reactions"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "A list of the genes encoded in the model can be accessed via `model.genes`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<Gene b0002 at 0x103f25748>,\n",
       " <Gene b0003 at 0x1034ec2e8>,\n",
       " <Gene b0004 at 0x1034fe3c8>,\n",
       " <Gene b0007 at 0x1034fe438>,\n",
       " <Gene b0008 at 0x1034f4780>,\n",
       " <Gene b0009 at 0x1034f4c88>,\n",
       " <Gene b0019 at 0x11237cd30>,\n",
       " <Gene b0025 at 0x11237cd68>,\n",
       " <Gene b0026 at 0x11237cda0>,\n",
       " <Gene b0029 at 0x11237cdd8>]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model.genes[0:10]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Other additional attributes can be accessed to explore the model. For example, exchange reactions that allow certain metabolites to enter or leave the model can be accessed through `model.exchanges`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<Reaction DM_4crsol_c at 0x1125f7160>,\n",
       " <Reaction DM_5drib_c at 0x1125f7470>,\n",
       " <Reaction DM_aacald_c at 0x1125f74a8>,\n",
       " <Reaction DM_amob_c at 0x1125f75c0>,\n",
       " <Reaction DM_mththf_c at 0x1125f75f8>,\n",
       " <Reaction DM_oxam_c at 0x1125f7630>,\n",
       " <Reaction EX_12ppd__R_e at 0x112613438>,\n",
       " <Reaction EX_12ppd__S_e at 0x112613470>,\n",
       " <Reaction EX_14glucan_e at 0x112613668>,\n",
       " <Reaction EX_15dap_e at 0x112613780>]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model.exchanges[0:10]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Or, the current medium can be accessed through `model.medium`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'EX_ca2_e': 1000.0,\n",
       " 'EX_cbl1_e': 0.01,\n",
       " 'EX_cl_e': 1000.0,\n",
       " 'EX_co2_e': 1000.0,\n",
       " 'EX_cobalt2_e': 1000.0,\n",
       " 'EX_cu2_e': 1000.0,\n",
       " 'EX_fe2_e': 1000.0,\n",
       " 'EX_fe3_e': 1000.0,\n",
       " 'EX_glc__D_e': 10.0,\n",
       " 'EX_h2o_e': 1000.0,\n",
       " 'EX_h_e': 1000.0,\n",
       " 'EX_k_e': 1000.0,\n",
       " 'EX_mg2_e': 1000.0,\n",
       " 'EX_mn2_e': 1000.0,\n",
       " 'EX_mobd_e': 1000.0,\n",
       " 'EX_na1_e': 1000.0,\n",
       " 'EX_nh4_e': 1000.0,\n",
       " 'EX_ni2_e': 1000.0,\n",
       " 'EX_o2_e': 1000.0,\n",
       " 'EX_pi_e': 1000.0,\n",
       " 'EX_sel_e': 1000.0,\n",
       " 'EX_slnt_e': 1000.0,\n",
       " 'EX_so4_e': 1000.0,\n",
       " 'EX_tungs_e': 1000.0,\n",
       " 'EX_zn2_e': 1000.0}"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model.medium"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "It is also possible to get a list of essential reactions ..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<Reaction THDPS at 0x1129fc080>,\n",
       " <Reaction UAAGDS at 0x112a1a080>,\n",
       " <Reaction PPNDH at 0x1129a60b8>,\n",
       " <Reaction CYSTL at 0x1125d40f0>,\n",
       " <Reaction E4PD at 0x112606160>,\n",
       " <Reaction KDOPP at 0x1126e2198>,\n",
       " <Reaction DHAD2 at 0x1125ea198>,\n",
       " <Reaction APRAUR at 0x1125881d0>,\n",
       " <Reaction METS at 0x11291e1d0>,\n",
       " <Reaction PAPPT3 at 0x11297c1d0>]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from cobra.flux_analysis import find_essential_reactions\n",
    "list(find_essential_reactions(model))[0:10]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "... and essential genes."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<Gene b1662 at 0x1123b6048>,\n",
       " <Gene b4245 at 0x112506128>,\n",
       " <Gene b3633 at 0x1123f0198>,\n",
       " <Gene b3634 at 0x1123f01d0>,\n",
       " <Gene b3639 at 0x1123f0208>,\n",
       " <Gene b4261 at 0x112506208>,\n",
       " <Gene b1415 at 0x1123ae240>,\n",
       " <Gene b4262 at 0x112506240>,\n",
       " <Gene b3642 at 0x1123f0278>,\n",
       " <Gene b1693 at 0x1123b6278>]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from cobra.flux_analysis import find_essential_genes\n",
    "list(find_essential_genes(model))[0:10]"
   ]
  }
 ],
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  "anaconda-cloud": {},
  "kernelspec": {
   "display_name": "Python 3",
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   "codemirror_mode": {
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