{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Single Model API\n",
    "\n",
    "## Building communities\n",
    "\n",
    "`micom` will construct communities from a specification via a Pandas DataFrame. Here, the DataFrame needs at least two columns: \"id\" and \"file\" which specify the ID of the organism/tissue and a file containing the actual individual model. \n",
    "\n",
    "To make more sense of that we can look at a small example. `micom` comes with a function that generates a simple example community specification consisting of several copies of a small *E. coli* model containing only the central carbon metabolism."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "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>id</th>\n",
       "      <th>genus</th>\n",
       "      <th>species</th>\n",
       "      <th>reactions</th>\n",
       "      <th>metabolites</th>\n",
       "      <th>file</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Escherichia_coli_1</td>\n",
       "      <td>Escherichia</td>\n",
       "      <td>Escherichia coli</td>\n",
       "      <td>95</td>\n",
       "      <td>72</td>\n",
       "      <td>/home/cdiener/code/micom/micom/data/e_coli_cor...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Escherichia_coli_2</td>\n",
       "      <td>Escherichia</td>\n",
       "      <td>Escherichia coli</td>\n",
       "      <td>95</td>\n",
       "      <td>72</td>\n",
       "      <td>/home/cdiener/code/micom/micom/data/e_coli_cor...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Escherichia_coli_3</td>\n",
       "      <td>Escherichia</td>\n",
       "      <td>Escherichia coli</td>\n",
       "      <td>95</td>\n",
       "      <td>72</td>\n",
       "      <td>/home/cdiener/code/micom/micom/data/e_coli_cor...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Escherichia_coli_4</td>\n",
       "      <td>Escherichia</td>\n",
       "      <td>Escherichia coli</td>\n",
       "      <td>95</td>\n",
       "      <td>72</td>\n",
       "      <td>/home/cdiener/code/micom/micom/data/e_coli_cor...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                   id        genus           species  reactions  metabolites  \\\n",
       "0  Escherichia_coli_1  Escherichia  Escherichia coli         95           72   \n",
       "1  Escherichia_coli_2  Escherichia  Escherichia coli         95           72   \n",
       "2  Escherichia_coli_3  Escherichia  Escherichia coli         95           72   \n",
       "3  Escherichia_coli_4  Escherichia  Escherichia coli         95           72   \n",
       "\n",
       "                                                file  \n",
       "0  /home/cdiener/code/micom/micom/data/e_coli_cor...  \n",
       "1  /home/cdiener/code/micom/micom/data/e_coli_cor...  \n",
       "2  /home/cdiener/code/micom/micom/data/e_coli_cor...  \n",
       "3  /home/cdiener/code/micom/micom/data/e_coli_cor...  "
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from micom.data import test_taxonomy\n",
    "\n",
    "taxonomy = test_taxonomy()\n",
    "taxonomy"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "As we see this specification contains the required fields and some more information. In fact the specification may contain any number of additional information which will be saved along with the community model. One special example is \"abundance\" which we will get to know soon :) The logic behind requiring the community information in this table format is that this table can be appended as supplement to your project or publication as is and describes your community composition without any doubt.\n",
    "\n",
    "In order to convert the specification in a community model we will use the `Community` class from `micom` which derives from the cobrapy `Model` class."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "f8eff43e337d440fa048416040171fed",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "HBox(children=(FloatProgress(value=0.0, max=4.0), HTML(value='')))"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "Build a community with a total of 400 reactions.\n"
     ]
    }
   ],
   "source": [
    "from micom import Community\n",
    "\n",
    "com = Community(taxonomy)\n",
    "print(\"Build a community with a total of {} reactions.\".format(len(com.reactions)))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This includes the correctly scaled exchange reactions with the internal medium and initializes the external imports to the maximum found in all models. The original taxonomy is maintained in the `com.taxonomy` attribute.\n",
    "\n",
    "Note that `micom` can figure out how to read a variety of different file types based on the extension. It curently supports:\n",
    "\n",
    "- `.pickle` for pickled models\n",
    "- `.xml` or `.gz` for XML models\n",
    "- `.json` for JSON models\n",
    "- `.mat` for COBRAtoolbox models\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "        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>id</th>\n",
       "      <th>genus</th>\n",
       "      <th>species</th>\n",
       "      <th>reactions</th>\n",
       "      <th>metabolites</th>\n",
       "      <th>file</th>\n",
       "      <th>abundance</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>id</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>Escherichia_coli_1</th>\n",
       "      <td>Escherichia_coli_1</td>\n",
       "      <td>Escherichia</td>\n",
       "      <td>Escherichia coli</td>\n",
       "      <td>95</td>\n",
       "      <td>72</td>\n",
       "      <td>/home/cdiener/code/micom/micom/data/e_coli_cor...</td>\n",
       "      <td>0.25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Escherichia_coli_2</th>\n",
       "      <td>Escherichia_coli_2</td>\n",
       "      <td>Escherichia</td>\n",
       "      <td>Escherichia coli</td>\n",
       "      <td>95</td>\n",
       "      <td>72</td>\n",
       "      <td>/home/cdiener/code/micom/micom/data/e_coli_cor...</td>\n",
       "      <td>0.25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Escherichia_coli_3</th>\n",
       "      <td>Escherichia_coli_3</td>\n",
       "      <td>Escherichia</td>\n",
       "      <td>Escherichia coli</td>\n",
       "      <td>95</td>\n",
       "      <td>72</td>\n",
       "      <td>/home/cdiener/code/micom/micom/data/e_coli_cor...</td>\n",
       "      <td>0.25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Escherichia_coli_4</th>\n",
       "      <td>Escherichia_coli_4</td>\n",
       "      <td>Escherichia</td>\n",
       "      <td>Escherichia coli</td>\n",
       "      <td>95</td>\n",
       "      <td>72</td>\n",
       "      <td>/home/cdiener/code/micom/micom/data/e_coli_cor...</td>\n",
       "      <td>0.25</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                    id        genus           species  \\\n",
       "id                                                                      \n",
       "Escherichia_coli_1  Escherichia_coli_1  Escherichia  Escherichia coli   \n",
       "Escherichia_coli_2  Escherichia_coli_2  Escherichia  Escherichia coli   \n",
       "Escherichia_coli_3  Escherichia_coli_3  Escherichia  Escherichia coli   \n",
       "Escherichia_coli_4  Escherichia_coli_4  Escherichia  Escherichia coli   \n",
       "\n",
       "                    reactions  metabolites  \\\n",
       "id                                           \n",
       "Escherichia_coli_1         95           72   \n",
       "Escherichia_coli_2         95           72   \n",
       "Escherichia_coli_3         95           72   \n",
       "Escherichia_coli_4         95           72   \n",
       "\n",
       "                                                                 file  \\\n",
       "id                                                                      \n",
       "Escherichia_coli_1  /home/cdiener/code/micom/micom/data/e_coli_cor...   \n",
       "Escherichia_coli_2  /home/cdiener/code/micom/micom/data/e_coli_cor...   \n",
       "Escherichia_coli_3  /home/cdiener/code/micom/micom/data/e_coli_cor...   \n",
       "Escherichia_coli_4  /home/cdiener/code/micom/micom/data/e_coli_cor...   \n",
       "\n",
       "                    abundance  \n",
       "id                             \n",
       "Escherichia_coli_1       0.25  \n",
       "Escherichia_coli_2       0.25  \n",
       "Escherichia_coli_3       0.25  \n",
       "Escherichia_coli_4       0.25  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "com.taxonomy"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "As you can notice we have gained a new column called `abundance`. This column quantifies the relative quantity of each individual in the community. Since we did not specify this in the original taxonomy `micom` assumes that all individuals are present in the same quantity."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The presented community here is pretty simplistic. For microbial communities `micom` includes a larger taxonomy for 773 microbial species from the [AGORA paper](https://doi.org/10.1038/nbt.3703). Here the \"file\" column only contains the base names for the files but you can easily prepend any path as demonstrated in the following:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "        vertical-align: middle;\n",
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       "\n",
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       "    }\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>organism</th>\n",
       "      <th>seedid</th>\n",
       "      <th>kingdom</th>\n",
       "      <th>phylum</th>\n",
       "      <th>mclass</th>\n",
       "      <th>order</th>\n",
       "      <th>family</th>\n",
       "      <th>genus</th>\n",
       "      <th>oxygenstat</th>\n",
       "      <th>metabolism</th>\n",
       "      <th>...</th>\n",
       "      <th>draftcreated</th>\n",
       "      <th>phenotype</th>\n",
       "      <th>imgid</th>\n",
       "      <th>ncbiid</th>\n",
       "      <th>platform</th>\n",
       "      <th>kbaseid</th>\n",
       "      <th>species</th>\n",
       "      <th>file</th>\n",
       "      <th>id</th>\n",
       "      <th>taxa_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Abiotrophia defectiva ATCC 49176</td>\n",
       "      <td>Abiotrophia defectiva ATCC 49176 (592010.4)</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>Firmicutes</td>\n",
       "      <td>Bacilli</td>\n",
       "      <td>Lactobacillales</td>\n",
       "      <td>Aerococcaceae</td>\n",
       "      <td>Abiotrophia</td>\n",
       "      <td>Facultative anaerobe</td>\n",
       "      <td>Saccharolytic, fermentative or respiratory</td>\n",
       "      <td>...</td>\n",
       "      <td>07/01/14</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.562617e+09</td>\n",
       "      <td>592010.0</td>\n",
       "      <td>ModelSEED</td>\n",
       "      <td>NaN</td>\n",
       "      <td>defectiva</td>\n",
       "      <td>models/Abiotrophia_defectiva_ATCC_49176.xml</td>\n",
       "      <td>Abiotrophia_defectiva_ATCC_49176</td>\n",
       "      <td>46125.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Achromobacter xylosoxidans A8</td>\n",
       "      <td>Achromobacter xylosoxidans A8 (762376.5)</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>Proteobacteria</td>\n",
       "      <td>Betaproteobacteria</td>\n",
       "      <td>Burkholderiales</td>\n",
       "      <td>Alcaligenaceae</td>\n",
       "      <td>Achromobacter</td>\n",
       "      <td>Aerobe</td>\n",
       "      <td>Respiratory</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>762376.0</td>\n",
       "      <td>ModelSEED</td>\n",
       "      <td>kb_g_3268_model_gf</td>\n",
       "      <td>xylosoxidans</td>\n",
       "      <td>models/Achromobacter_xylosoxidans_A8.xml</td>\n",
       "      <td>Achromobacter_xylosoxidans_A8</td>\n",
       "      <td>85698.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Achromobacter xylosoxidans NBRC 15126 = ATCC 2...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>Proteobacteria</td>\n",
       "      <td>Betaproteobacteria</td>\n",
       "      <td>Burkholderiales</td>\n",
       "      <td>Alcaligenaceae</td>\n",
       "      <td>Achromobacter</td>\n",
       "      <td>Aerobe</td>\n",
       "      <td>Respiratory</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1216976.0</td>\n",
       "      <td>Kbase</td>\n",
       "      <td>kb|g.208127</td>\n",
       "      <td>xylosoxidans</td>\n",
       "      <td>models/Achromobacter_xylosoxidans_NBRC_15126.xml</td>\n",
       "      <td>Achromobacter_xylosoxidans_NBRC_15126</td>\n",
       "      <td>85698.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Acidaminococcus fermentans DSM 20731</td>\n",
       "      <td>Acidaminococcus fermentans DSM 20731 (591001.3)</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>Firmicutes</td>\n",
       "      <td>Negativicutes</td>\n",
       "      <td>Acidaminococcales</td>\n",
       "      <td>Acidaminococcaceae</td>\n",
       "      <td>Acidaminococcus</td>\n",
       "      <td>Obligate anaerobe</td>\n",
       "      <td>Fermentative</td>\n",
       "      <td>...</td>\n",
       "      <td>04/17/16</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6.463119e+08</td>\n",
       "      <td>591001.0</td>\n",
       "      <td>Kbase</td>\n",
       "      <td>kb|g.2555</td>\n",
       "      <td>fermentans</td>\n",
       "      <td>models/Acidaminococcus_fermentans_DSM_20731.xml</td>\n",
       "      <td>Acidaminococcus_fermentans_DSM_20731</td>\n",
       "      <td>905.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Acidaminococcus intestini RyC-MR95</td>\n",
       "      <td>Acidaminococcus intestini RyC-MR95 (568816.4)</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>Firmicutes</td>\n",
       "      <td>Negativicutes</td>\n",
       "      <td>Selenomonadales</td>\n",
       "      <td>Acidaminococcaceae</td>\n",
       "      <td>Acidaminococcus</td>\n",
       "      <td>Obligate anaerobe</td>\n",
       "      <td>Asaccharolytic, glutamate is fermented</td>\n",
       "      <td>...</td>\n",
       "      <td>08/03/14</td>\n",
       "      <td>4.0</td>\n",
       "      <td>2.511231e+09</td>\n",
       "      <td>568816.0</td>\n",
       "      <td>Kbase</td>\n",
       "      <td>NaN</td>\n",
       "      <td>intestini</td>\n",
       "      <td>models/Acidaminococcus_intestini_RyC_MR95.xml</td>\n",
       "      <td>Acidaminococcus_intestini_RyC_MR95</td>\n",
       "      <td>187327.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 26 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                            organism  \\\n",
       "0                   Abiotrophia defectiva ATCC 49176   \n",
       "1                      Achromobacter xylosoxidans A8   \n",
       "2  Achromobacter xylosoxidans NBRC 15126 = ATCC 2...   \n",
       "3               Acidaminococcus fermentans DSM 20731   \n",
       "4                 Acidaminococcus intestini RyC-MR95   \n",
       "\n",
       "                                            seedid   kingdom          phylum  \\\n",
       "0      Abiotrophia defectiva ATCC 49176 (592010.4)  Bacteria      Firmicutes   \n",
       "1         Achromobacter xylosoxidans A8 (762376.5)  Bacteria  Proteobacteria   \n",
       "2                                              NaN  Bacteria  Proteobacteria   \n",
       "3  Acidaminococcus fermentans DSM 20731 (591001.3)  Bacteria      Firmicutes   \n",
       "4    Acidaminococcus intestini RyC-MR95 (568816.4)  Bacteria      Firmicutes   \n",
       "\n",
       "               mclass              order              family            genus  \\\n",
       "0             Bacilli    Lactobacillales       Aerococcaceae      Abiotrophia   \n",
       "1  Betaproteobacteria    Burkholderiales      Alcaligenaceae    Achromobacter   \n",
       "2  Betaproteobacteria    Burkholderiales      Alcaligenaceae    Achromobacter   \n",
       "3       Negativicutes  Acidaminococcales  Acidaminococcaceae  Acidaminococcus   \n",
       "4       Negativicutes    Selenomonadales  Acidaminococcaceae  Acidaminococcus   \n",
       "\n",
       "             oxygenstat                                  metabolism  ...  \\\n",
       "0  Facultative anaerobe  Saccharolytic, fermentative or respiratory  ...   \n",
       "1                Aerobe                                 Respiratory  ...   \n",
       "2                Aerobe                                 Respiratory  ...   \n",
       "3     Obligate anaerobe                                Fermentative  ...   \n",
       "4     Obligate anaerobe      Asaccharolytic, glutamate is fermented  ...   \n",
       "\n",
       "  draftcreated phenotype         imgid     ncbiid   platform  \\\n",
       "0     07/01/14       1.0  2.562617e+09   592010.0  ModelSEED   \n",
       "1          NaN       NaN           NaN   762376.0  ModelSEED   \n",
       "2          NaN       NaN           NaN  1216976.0      Kbase   \n",
       "3     04/17/16       NaN  6.463119e+08   591001.0      Kbase   \n",
       "4     08/03/14       4.0  2.511231e+09   568816.0      Kbase   \n",
       "\n",
       "              kbaseid       species  \\\n",
       "0                 NaN     defectiva   \n",
       "1  kb_g_3268_model_gf  xylosoxidans   \n",
       "2         kb|g.208127  xylosoxidans   \n",
       "3           kb|g.2555    fermentans   \n",
       "4                 NaN     intestini   \n",
       "\n",
       "                                               file  \\\n",
       "0       models/Abiotrophia_defectiva_ATCC_49176.xml   \n",
       "1          models/Achromobacter_xylosoxidans_A8.xml   \n",
       "2  models/Achromobacter_xylosoxidans_NBRC_15126.xml   \n",
       "3   models/Acidaminococcus_fermentans_DSM_20731.xml   \n",
       "4     models/Acidaminococcus_intestini_RyC_MR95.xml   \n",
       "\n",
       "                                      id   taxa_id  \n",
       "0       Abiotrophia_defectiva_ATCC_49176   46125.0  \n",
       "1          Achromobacter_xylosoxidans_A8   85698.0  \n",
       "2  Achromobacter_xylosoxidans_NBRC_15126   85698.0  \n",
       "3   Acidaminococcus_fermentans_DSM_20731     905.0  \n",
       "4     Acidaminococcus_intestini_RyC_MR95  187327.0  \n",
       "\n",
       "[5 rows x 26 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from micom.data import agora\n",
    "\n",
    "tax = agora.copy()\n",
    "tax.file = \"models/\" + tax.file  # assuming you have downloaded the AGORA models to the \"models\" folder\n",
    "tax.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Saving and loading communities\n",
    "\n",
    "Contructing large community models can be slow which is due to performance limitations of the solvers. In essence, adding a single variable/constraint to a model qih 10 variables is much faster than adding it to a model with 10 million variables. Thus, we recommend you save the constructed community in a serialized format afterwards which will be much faster in loading repetitively."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "2a381ea543bd4803bdeb7eadd021cd2f",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "HBox(children=(FloatProgress(value=0.0, max=4.0), HTML(value='')))"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "CPU times: user 756 ms, sys: 12.6 ms, total: 768 ms\n",
      "Wall time: 776 ms\n"
     ]
    }
   ],
   "source": [
    "%time com = Community(taxonomy)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 77.8 ms, sys: 3.77 ms, total: 81.6 ms\n",
      "Wall time: 81.4 ms\n"
     ]
    }
   ],
   "source": [
    "%time com.to_pickle(\"community.pickle\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 36.4 ms, sys: 7.71 ms, total: 44.1 ms\n",
      "Wall time: 43.6 ms\n"
     ]
    }
   ],
   "source": [
    "from micom import load_pickle\n",
    "%time com = load_pickle(\"community.pickle\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "As we can see loading the model from the pickle format is much faster than creating it *de novo*."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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