en/example5.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# A Simple Model of the Glycolysis of Human Erythrocytes\n",
    "\n",
    "This is a model for the glycolysis of human erythrocytes which takes into account ATP-synthesis and -consumption.\n",
    "This model is based on the model introduced in the following publication.\n",
    "\n",
    "* Rapoport, T.A. and Heinrich, R. (1975) \"Mathematical analysis of multienzyme systems. I. Modelling of the glycolysis of human erythrocytes.\", Biosystems., 7, 1, 120-129. \n",
    "* Heinrich, R. and Rapoport, T.A. (1975) \"Mathematical analysis of multienzyme systems. II. Steady state and transient control.\", Biosystems., 7, 1, 130-136."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "from ecell4 import *\n",
    "util.decorator.ENABLE_RATELAW = True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "with reaction_rules():\n",
    "    2 * ATP > 2 * A13P2G + 2 * ADP | (3.2 * ATP / (1.0 + (ATP / 1.0) ** 4.0))\n",
    "    A13P2G > A23P2G | 1500\n",
    "    A23P2G > PEP | 0.15\n",
    "    A13P2G + ADP > PEP + ATP | 1.57e+4\n",
    "    PEP + ADP > ATP | 559\n",
    "    AMP + ATP > 2 * ADP | (1.0 * (AMP * ATP - 2.0 * ADP * ADP))\n",
    "    ATP > ADP | 1.46"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "y0 = {\"A13P2G\": 0.0005082, \"A23P2G\": 5.0834, \"PEP\": 0.020502,\n",
    "      \"AMP\": 0.080139, \"ADP\": 0.2190, \"ATP\": 1.196867}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
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5oBnwgJK+iEj+5fXNXRERyb28vbkb5Ze7zOwIM5trZivNbIWZjUpub2dmL5rZ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\nHtoUu0bmuAAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7f7fe1b99350>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "run_simulation(100, y0=y0)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}