Wataru Reversible.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "from ecell4 import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "kf, kr = 0.01, 5\n",
    "\n",
    "with reaction_rules():\n",
    "    A + B == C | (kf, kr)\n",
    "\n",
    "m = get_model()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "obs = run_simulation(0.5, model=m, y0={'A': 1000, 'B': 1000}, return_type='observer')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "image/png": 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fDW5pPeAA6N8f9t8/KLvsopqESAMU5fAkLdx9ulU+8ejuZtbg5vOQNCkrC2oU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\n/x9UgO/WvNTj6AAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7f3c00a36250>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "viz.plot_number_observer(obs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[[0.0, 1000.0, 1000.0, 0.0], [0.005, 952.9619272410331, 952.9619272410331, 47.038072758966834], [0.01, 911.2589587313197, 911.2589587313197, 88.74104126868032], [0.015, 874.1310050809262, 874.1310050809262, 125.8689949190737], [0.02, 840.9528626055019, 840.9528626055019, 159.0471373944982], [0.025, 811.2055468723977, 811.2055468723977, 188.79445312760242], [0.03, 784.4546374863486, 784.4546374863486, 215.54536251365155], [0.035, 760.3337247789004, 760.3337247789004, 239.6662752210997], [0.04, 738.5316045103419, 738.5316045103419, 261.4683954896582], [0.045, 718.7822677106117, 718.7822677106117, 281.21773228938844], [0.05, 700.8570004317878, 700.8570004317878, 299.1429995682122], [0.055, 684.5580858660112, 684.5580858660112, 315.441914133989], [0.06, 669.7137482849246, 669.7137482849246, 330.2862517150756], [0.065, 656.1740581796001, 656.1740581796001, 343.8259418204001], [0.07, 643.8075923028366, 643.8075923028366, 356.1924076971637], [0.075, 632.4986917272291, 632.4986917272291, 367.5013082727713], [0.08, 622.1451953016083, 622.1451953016083, 377.8548046983923], [0.085, 612.6565545822289, 612.6565545822289, 387.3434454177719], [0.09, 603.9522589591008, 603.9522589591008, 396.0477410409], [0.095, 595.9605105339813, 595.9605105339813, 404.0394894660195], [0.1, 588.6171049980892, 588.6171049980892, 411.3828950019116], [0.105, 581.8644810606529, 581.8644810606529, 418.1355189393477], [0.11, 575.6509103606536, 575.6509103606536, 424.3490896393469], [0.115, 569.9298026678548, 569.9298026678548, 430.07019733214565], [0.12, 564.659109120942, 564.659109120942, 435.34089087905846], [0.125, 559.8008061969908, 559.8008061969908, 440.1991938030098], [0.13, 555.320448896777, 555.320448896777, 444.6795511032237], [0.135, 551.1867815787966, 551.1867815787966, 448.81321842120406], [0.14, 547.3713987353549, 547.3713987353549, 452.6286012646458], [0.145, 543.8484476961256, 543.8484476961256, 456.1515523038753], [0.15, 540.5943674476073, 540.5943674476073, 459.4056325523937], [0.155, 537.5876584622814, 537.5876584622814, 462.41234153771967], [0.16, 534.8086795195175, 534.8086795195175, 465.1913204804835], [0.165, 532.2394676224727, 532.2394676224727, 467.7605323775282], [0.17, 529.8635777935614, 529.8635777935614, 470.1364222064395], [0.175, 527.6659407454916, 527.6659407454916, 472.3340592545092], [0.18, 525.6327357194148, 525.6327357194148, 474.367264280586], [0.185, 523.7512766485419, 523.7512766485419, 476.24872335145903], [0.19, 522.0099102100457, 522.0099102100457, 477.9900897899552], [0.195, 520.3979242016196, 520.3979242016196, 479.60207579838135], [0.2, 518.9054650697311, 518.9054650697311, 481.0945349302697], [0.205, 517.523463561014, 517.523463561014, 482.4765364389868], [0.21, 516.2435676455323, 516.2435676455323, 483.75643235446853], [0.215, 515.0580816201602, 515.0580816201602, 484.94191837984056], [0.22, 513.9599111774879, 513.9599111774879, 486.0400888225129], [0.225, 512.9425133268563, 512.9425133268563, 487.05748667314435], [0.23, 511.99985109976586, 511.99985109976586, 488.00014890023493], [0.235, 511.12635218353375, 511.12635218353375, 488.873647816467], [0.24, 510.316871275702, 510.316871275702, 489.6831287242988], [0.245, 509.56665576342766, 509.56665576342766, 490.43334423657313], [0.25, 508.87131437081337, 508.87131437081337, 491.12868562918743], [0.255, 508.22678850440514, 508.22678850440514, 491.77321149559566], [0.26, 507.6293260133923, 507.6293260133923, 492.3706739866085], [0.265, 507.075457209479, 507.075457209479, 492.9245427905218], [0.27, 506.5619728199914, 506.5619728199914, 493.4380271800094], [0.275, 506.08590381887615, 506.08590381887615, 493.91409618112465], [0.28, 505.6445028675475, 505.6445028675475, 494.3554971324533], [0.285, 505.23522731833316, 505.23522731833316, 494.76477268166764], [0.29, 504.855723503908, 504.855723503908, 495.1442764960928], [0.295, 504.5038123954016, 504.5038123954016, 495.4961876045992], [0.3, 504.1774763057178, 504.1774763057178, 495.822523694283], [0.305, 503.8748466933718, 503.8748466933718, 496.125153306629], [0.31, 503.59419291226715, 503.59419291226715, 496.40580708773365], [0.315, 503.33391185041404, 503.33391185041404, 496.66608814958676], [0.32, 503.0925183571505, 503.0925183571505, 496.9074816428503], [0.325, 502.8686364279041, 502.8686364279041, 497.1313635720967], [0.33, 502.6609910558184, 502.6609910558184, 497.3390089441824], [0.335, 502.4684007177496, 502.4684007177496, 497.5315992822512], [0.34, 502.28977042549906, 502.28977042549906, 497.71022957450174], [0.345, 502.1240853139222, 502.1240853139222, 497.8759146860786], [0.35, 501.9704047087509, 501.9704047087509, 498.0295952912499], [0.355, 501.8278566445335, 501.8278566445335, 498.1721433554673], [0.36, 501.695632798587, 501.695632798587, 498.3043672014138], [0.365, 501.57298380480705, 501.57298380480705, 498.42701619519374], [0.37, 501.4592149133978, 501.4592149133978, 498.540785086603], [0.375, 501.35368198043307, 501.35368198043307, 498.64631801956773], [0.38, 501.2557877545194, 501.2557877545194, 498.7442122454814], [0.385, 501.164978438493, 501.164978438493, 498.8350215615078], [0.39, 501.0807405113725, 501.0807405113725, 498.9192594886283], [0.395, 501.00259777662086, 501.00259777662086, 498.99740222337994], [0.4, 500.93010863790784, 500.93010863790784, 499.06989136209296], [0.405, 500.8628635721343, 500.8628635721343, 499.1371364278665], [0.41, 500.8004827879716, 500.8004827879716, 499.1995172120292], [0.415, 500.74261405868907, 500.74261405868907, 499.2573859413117], [0.42, 500.68893071186045, 500.68893071186045, 499.31106928814035], [0.425, 500.6391297712777, 500.6391297712777, 499.3608702287231], [0.43, 500.59293022822106, 500.59293022822106, 499.40706977177973], [0.435, 500.55007144737493, 500.55007144737493, 499.44992855262586], [0.44, 500.51031168111535, 500.51031168111535, 499.48968831888544], [0.445, 500.47342670161044, 500.47342670161044, 499.52657329839036], [0.45, 500.4392085229324, 500.4392085229324, 499.5607914770684], [0.455, 500.40746422630644, 500.40746422630644, 499.59253577369435], [0.46, 500.37801486292597, 500.37801486292597, 499.62198513707483], [0.465, 500.3506944415535, 500.3506944415535, 499.6493055584473], [0.47, 500.32534898840805, 500.32534898840805, 499.67465101159274], [0.475, 500.3018356748858, 500.3018356748858, 499.698164325115], [0.48, 500.28002201047286, 500.28002201047286, 499.71997798952793], [0.485, 500.25978509251973, 500.25978509251973, 499.74021490748106], [0.49, 500.2410109117192, 500.2410109117192, 499.7589890882816], [0.495, 500.2235937079494, 500.2235937079494, 499.7764062920514], [0.5, 500.2074353725009, 500.2074353725009, 499.79256462749987]]\n"
     ]
    }
   ],
   "source": [
    "print(obs.data())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "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
}