docs/notebooks/Model_manipulation.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Getting and setting reaction parameters and reactions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "sys.path.append('../..')\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from basico import *"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Load model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "biomod = load_example(\"LM-test1\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Getting/setting global quantities"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "        It is possible to set:\n",
    "            'initial_value'\n",
    "            'initial_expression'\n",
    "            'expression'\n",
    "            'status'\n",
    "            'type'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>unit</th>\n",
       "      <th>initial_value</th>\n",
       "      <th>initial_expression</th>\n",
       "      <th>expression</th>\n",
       "      <th>value</th>\n",
       "      <th>rate</th>\n",
       "      <th>key</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></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>epsilon</th>\n",
       "      <td>fixed</td>\n",
       "      <td></td>\n",
       "      <td>0.78</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>ModelValue_0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>offset</th>\n",
       "      <td>fixed</td>\n",
       "      <td></td>\n",
       "      <td>0.10</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>ModelValue_1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>signal</th>\n",
       "      <td>assignment</td>\n",
       "      <td></td>\n",
       "      <td>0.10</td>\n",
       "      <td></td>\n",
       "      <td>[P] * Values[epsilon] + Values[offset]</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>ModelValue_2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "               type unit  initial_value initial_expression  \\\n",
       "name                                                         \n",
       "epsilon       fixed                0.78                      \n",
       "offset        fixed                0.10                      \n",
       "signal   assignment                0.10                      \n",
       "\n",
       "                                     expression  value  rate           key  \n",
       "name                                                                        \n",
       "epsilon                                            NaN   0.0  ModelValue_0  \n",
       "offset                                             NaN   0.0  ModelValue_1  \n",
       "signal   [P] * Values[epsilon] + Values[offset]    NaN   NaN  ModelValue_2  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_parameters()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "set_parameters(name= 'offset', initial_value = 50)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "set_parameters('signal', expression='[P] * Values[epsilon] + Values[offset]')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
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       "      <th>initial_value</th>\n",
       "      <th>initial_expression</th>\n",
       "      <th>expression</th>\n",
       "      <th>value</th>\n",
       "      <th>rate</th>\n",
       "      <th>key</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
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       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>epsilon</th>\n",
       "      <td>fixed</td>\n",
       "      <td></td>\n",
       "      <td>0.78</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>ModelValue_0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>offset</th>\n",
       "      <td>fixed</td>\n",
       "      <td></td>\n",
       "      <td>50.00</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>ModelValue_1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>signal</th>\n",
       "      <td>assignment</td>\n",
       "      <td></td>\n",
       "      <td>50.00</td>\n",
       "      <td></td>\n",
       "      <td>[P] * Values[epsilon] + Values[offset]</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>ModelValue_2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "               type unit  initial_value initial_expression  \\\n",
       "name                                                         \n",
       "epsilon       fixed                0.78                      \n",
       "offset        fixed               50.00                      \n",
       "signal   assignment               50.00                      \n",
       "\n",
       "                                     expression  value  rate           key  \n",
       "name                                                                        \n",
       "epsilon                                            NaN   0.0  ModelValue_0  \n",
       "offset                                             NaN   0.0  ModelValue_1  \n",
       "signal   [P] * Values[epsilon] + Values[offset]    NaN   NaN  ModelValue_2  "
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_parameters()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Getting/setting species (metabolites)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>compartment</th>\n",
       "      <th>type</th>\n",
       "      <th>unit</th>\n",
       "      <th>initial_concentration</th>\n",
       "      <th>initial_particle_number</th>\n",
       "      <th>initial_expression</th>\n",
       "      <th>expression</th>\n",
       "      <th>concentration</th>\n",
       "      <th>particle_number</th>\n",
       "      <th>rate</th>\n",
       "      <th>particle_number_rate</th>\n",
       "      <th>key</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></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>E</th>\n",
       "      <td>compartment</td>\n",
       "      <td>reactions</td>\n",
       "      <td>mmol/ml</td>\n",
       "      <td>0.010000</td>\n",
       "      <td>6.022142e+18</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Metabolite_1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>S</th>\n",
       "      <td>compartment</td>\n",
       "      <td>reactions</td>\n",
       "      <td>mmol/ml</td>\n",
       "      <td>10.000001</td>\n",
       "      <td>6.022142e+21</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Metabolite_0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ES</th>\n",
       "      <td>compartment</td>\n",
       "      <td>reactions</td>\n",
       "      <td>mmol/ml</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Metabolite_2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P</th>\n",
       "      <td>compartment</td>\n",
       "      <td>reactions</td>\n",
       "      <td>mmol/ml</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Metabolite_3</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      compartment       type     unit  initial_concentration  \\\n",
       "name                                                           \n",
       "E     compartment  reactions  mmol/ml               0.010000   \n",
       "S     compartment  reactions  mmol/ml              10.000001   \n",
       "ES    compartment  reactions  mmol/ml               0.000000   \n",
       "P     compartment  reactions  mmol/ml               0.000000   \n",
       "\n",
       "      initial_particle_number initial_expression expression  concentration  \\\n",
       "name                                                                         \n",
       "E                6.022142e+18                                          NaN   \n",
       "S                6.022142e+21                                          NaN   \n",
       "ES               0.000000e+00                                          NaN   \n",
       "P                0.000000e+00                                          NaN   \n",
       "\n",
       "      particle_number  rate  particle_number_rate           key  \n",
       "name                                                             \n",
       "E                 NaN   NaN                   NaN  Metabolite_1  \n",
       "S                 NaN   NaN                   NaN  Metabolite_0  \n",
       "ES                NaN   NaN                   NaN  Metabolite_2  \n",
       "P                 NaN   NaN                   NaN  Metabolite_3  "
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_species()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "E     0.01\n",
       "ES    0.00\n",
       "Name: initial_concentration, dtype: float64"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_species(name = 'E')['initial_concentration']"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Setting"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "        if 'name' in kwargs:\n",
    "            metab.setObjectName(kwargs['name'])\n",
    "\n",
    "        if 'unit' in kwargs:\n",
    "            metab.setUnitExpression(kwargs['unit'])\n",
    "\n",
    "        if 'initial_concentration' in kwargs:\n",
    "            metab.setInitialConcentration(kwargs['initial_concentration']),\n",
    "\n",
    "        if 'initial_particle_number' in kwargs:\n",
    "            metab.setInitialValue(kwargs['initial_particle_number']),\n",
    "\n",
    "        if 'initial_expression' in kwargs:\n",
    "            metab.setInitialExpression(kwargs['initial_expression'])\n",
    "\n",
    "        if 'expression' in kwargs:\n",
    "            metab.setExpression(kwargs['expression'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "set_species(name = 'E', new_name = 'Lilija')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "set_species(name = 'Lilija', initial_concentration = 123456)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>compartment</th>\n",
       "      <th>type</th>\n",
       "      <th>unit</th>\n",
       "      <th>initial_concentration</th>\n",
       "      <th>initial_particle_number</th>\n",
       "      <th>initial_expression</th>\n",
       "      <th>expression</th>\n",
       "      <th>concentration</th>\n",
       "      <th>particle_number</th>\n",
       "      <th>rate</th>\n",
       "      <th>particle_number_rate</th>\n",
       "      <th>key</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></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>Lilija</th>\n",
       "      <td>compartment</td>\n",
       "      <td>reactions</td>\n",
       "      <td>mmol/ml</td>\n",
       "      <td>123456.0</td>\n",
       "      <td>7.434694e+25</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Metabolite_1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "        compartment       type     unit  initial_concentration  \\\n",
       "name                                                             \n",
       "Lilija  compartment  reactions  mmol/ml               123456.0   \n",
       "\n",
       "        initial_particle_number initial_expression expression  concentration  \\\n",
       "name                                                                           \n",
       "Lilija             7.434694e+25                                          NaN   \n",
       "\n",
       "        particle_number  rate  particle_number_rate           key  \n",
       "name                                                               \n",
       "Lilija              NaN   NaN                   NaN  Metabolite_1  "
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_species(name = 'Lilija')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# change it back\n",
    "set_species(new_name = 'E', name = 'Lilija')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Getting/setting reaction parameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>value</th>\n",
       "      <th>reaction</th>\n",
       "      <th>type</th>\n",
       "      <th>mapped_to</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R1).k1</th>\n",
       "      <td>130.0</td>\n",
       "      <td>R1</td>\n",
       "      <td>local</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(R1).k2</th>\n",
       "      <td>1.0</td>\n",
       "      <td>R1</td>\n",
       "      <td>local</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(R2).k1</th>\n",
       "      <td>1.0</td>\n",
       "      <td>R2</td>\n",
       "      <td>local</td>\n",
       "      <td></td>\n",
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      ],
      "text/plain": [
       "         value reaction   type mapped_to\n",
       "name                                    \n",
       "(R1).k1  130.0       R1  local          \n",
       "(R1).k2    1.0       R1  local          \n",
       "(R2).k1    1.0       R2  local          "
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_reaction_parameters()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "        Setting only the following is possible:\n",
    "        'new_name'\n",
    "        'value'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "set_reaction_parameters(name = '(R1).k1', value=123)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>value</th>\n",
       "      <th>reaction</th>\n",
       "      <th>type</th>\n",
       "      <th>mapped_to</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R1).k1</th>\n",
       "      <td>123.0</td>\n",
       "      <td>R1</td>\n",
       "      <td>local</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(R1).k2</th>\n",
       "      <td>1.0</td>\n",
       "      <td>R1</td>\n",
       "      <td>local</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(R2).k1</th>\n",
       "      <td>1.0</td>\n",
       "      <td>R2</td>\n",
       "      <td>local</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "         value reaction   type mapped_to\n",
       "name                                    \n",
       "(R1).k1  123.0       R1  local          \n",
       "(R1).k2    1.0       R1  local          \n",
       "(R2).k1    1.0       R2  local          "
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_reaction_parameters()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Getting/setting reactions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>scheme</th>\n",
       "      <th>flux</th>\n",
       "      <th>particle_flux</th>\n",
       "      <th>function</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>R1</th>\n",
       "      <td>S + E = ES</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Mass action (reversible)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>R2</th>\n",
       "      <td>ES -&gt; E + P</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Mass action (irreversible)</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           scheme  flux  particle_flux                    function\n",
       "name                                                              \n",
       "R1     S + E = ES   NaN            NaN    Mass action (reversible)\n",
       "R2    ES -> E + P   NaN            NaN  Mass action (irreversible)"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_reactions()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Setting scheme"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "set_reaction(name = 'R1', scheme = 'S + E + F = ES')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>scheme</th>\n",
       "      <th>flux</th>\n",
       "      <th>particle_flux</th>\n",
       "      <th>function</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>R1</th>\n",
       "      <td>S + E + F = ES</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Mass action (reversible)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>R2</th>\n",
       "      <td>ES -&gt; E + P</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Mass action (irreversible)</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "              scheme  flux  particle_flux                    function\n",
       "name                                                                 \n",
       "R1    S + E + F = ES   NaN            NaN    Mass action (reversible)\n",
       "R2       ES -> E + P   NaN            NaN  Mass action (irreversible)"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_reactions()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Setting reaction name"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "set_reaction(name = 'R1', new_name = 'Reaction 1')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "      <th></th>\n",
       "      <th>scheme</th>\n",
       "      <th>flux</th>\n",
       "      <th>particle_flux</th>\n",
       "      <th>function</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>Reaction 1</th>\n",
       "      <td>S + E + F = ES</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Mass action (reversible)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>R2</th>\n",
       "      <td>ES -&gt; E + P</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Mass action (irreversible)</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                    scheme  flux  particle_flux                    function\n",
       "name                                                                       \n",
       "Reaction 1  S + E + F = ES   NaN            NaN    Mass action (reversible)\n",
       "R2             ES -> E + P   NaN            NaN  Mass action (irreversible)"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "get_reactions()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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