kozo2 · January 5, 2016 10:36
diff --git a/a.ipynb b/a.ipynb
 {
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 1. Brief Tour of E-Cell4 Simulations\n",
    "\n",
    "First of all, you have to load the E-Cell4 library:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "from ecell4 import *"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1.1. Quick Demostration\n",
    "\n",
    "There are three fundamental components consisting of E-Cell System version 4, which are `Model`, `World`, and `Simulator`. These components describe concepts in simulation.\n",
    "\n",
    "* `Model` describes a problem to simulate as its name suggests.  \n",
    "* `World` describes a state, e.g. an initial state and a state at a time-point.  \n",
    "* `Simulator` describes a solver.\n",
    "\n",
    "`Model` is independent from solvers. Every solver can share a single `Model` instance. Each alogrithm has a corresponding pair of `World` and `Simulator` (these pairs are capsulized into `Factory` class). `World` is not necessarily needed to be bound to `Model` and `Simulator`, but `Simulator` needs both `Model` and `World`.\n",
    "\n",
    "Before running a simulation, you have to make a `Model`. E-Cell4 supports multiple ways to buld a `Model` (See [2. How to Build a Model](2. How to Build a Model.ipynb)). Here, we explain the simplest way using the `with` statement with `reaction_rules`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<ecell4.core.NetworkModel object at 0x038FF9F0>\n"
     ]
    }
   ],
   "source": [
    "with reaction_rules():\n",
    "    A + B > C | 0.01  # equivalent to create_binding_reaction_rule\n",
    "    C > A + B | 0.3   # equivalent to create_unbinding_reaction_rule\n",
    "\n",
    "m1 = get_model()\n",
    "print(m1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Please remember to write parentheses `()` after `reaction_rules`. Here, a `Model` with two `ReactionRule`s named `m` was built. Lines in the `with` block describe `ReactionRule`s, a binding and unbinding reaction respectively. A kinetic rate for the mass action reaction is defined after a separator `|`, i.e. `0.01` or `0.3`. In the form of ordinary differential equations, this model can be described as:\n",
    "\n",
    "$$[\\mathrm{A}]'=[\\mathrm{B}]'=-[\\mathrm{C}]=-0.01[\\mathrm{A}][\\mathrm{B}]+0.3[\\mathrm{C}]$$"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For more compact description, `A + B == C | (0.01, 0.3)` is also acceptable.\n",
    "\n",
    "E-Cell4 has a simple interface to run simulations with the given model, `run_simulation`. This enables for you to run simulations without instanciate `World` and `Simulator` by yourself. To solve this model, you have to give a volume, an initial value for each `Species` and duration of time:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "c:\\python35\\lib\\site-packages\\matplotlib\\__init__.py:892: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.\n",
      "  warnings.warn(self.msg_depr % (key, alt_key))\n"
     ]
    },
    {
     "data": {
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QdVLnHsUkaWdgTES80u5F83KCsNpygrAaK3MU056SvgX8H6Bb0jcl7dnuhc3MrN7y9EH8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\nMjlBmJlZJicIMzPL9P8Byuqvlog12J8AAAAASUVORK5CYII=\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x5be6c30>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "run_simulation(10.0, model=m1, y0={'A': 60, 'B': 60}, volume=1.0)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To switch simulation algorithm, you only need to give the type of solver (`ode` is used as a default) as follows:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "c:\\python35\\lib\\site-packages\\matplotlib\\__init__.py:892: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.\n",
      "  warnings.warn(self.msg_depr % (key, alt_key))\n"
     ]
    },
    {
     "data": {
      "image/png": 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7eQRjZmbFyZIQXpF0AOnyEpLOBtblGpWZmdVclvsQ9geuBz4DvA6sAb7kLTTNMvCgshUg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\nCGZmBjghmJlZygnBzMwA+P9EfdIRUhy6iAAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x5b92e30>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "run_simulation(10.0, model=m1, y0={'A': 60, 'B': 60}, solver='gillespie')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1.2. Spatial Simulation and Visualization\n",
    "\n",
    "E-Cell4 now supports multiple spatial algorithms, `egfrd`, `spatiocyte` and `meso`. In addition to the model used in non-spatial solvers (`ode` and `gillespie`), these spatial solvers need extra information about each `Species`, i.e. a diffusion coefficient and radius.\n",
    "\n",
    "The `with` statement with `species_attributes` is available to describe these properties:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "with species_attributes():\n",
    "    A | B | C | {'radius': '0.005', 'D': '1'}  # 'D' is for the diffusion coefficient\n",
    "\n",
    "with reaction_rules():\n",
    "    A + B == C | (0.01, 0.3)\n",
    "\n",
    "m2 = get_model()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Even though the properties indicate a floating number, each attribute must be given as a string.\n",
    "\n",
    "Now you can run a spatial simulation in the same way as above (`egfrd` would need long time to simulate):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "c:\\python35\\lib\\site-packages\\matplotlib\\__init__.py:892: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.\n",
      "  warnings.warn(self.msg_depr % (key, alt_key))\n"
     ]
    },
    {
     "data": {
      "image/png": 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8BpxaZCgzM6tengIxLCIe6LTunSLCmJlZ88hTIF6R9FHS4TAknQy8VGgqMzOrXJ77IHYH\nrgY+B7wOPAN8xVOOmvWAL1JbiUqdcjTd4XZAS0S80ded5uUCYQOGC4SVqMxeTKMlfZ9kmO82SVdK\nGt3XHZuZWXPLcw3iR8DLwF8AJ6fLNxYZyszMqpfnGsQTEfHJTusej4h9C02GTzHZAOJTTFaiMof7\nXirpVEkt6WMasKSvOzYzs+bWsAUh6Q2Srq0CtgM2pS+1ABsiYkTh4dyCsIHCLQgrUeGjuUbE8L5u\n3MzMtlx5RnNF0n7AxPr3e7hvM7OBrdsCIemHwH7Ak7x3msnDfZuZDXB5WhAHRcTHC09iZmZNJU8v\npl9KcoEwMxtk8rQg5pEUiTXA2yS9miIi9is0mZmZVSpPgbgW+CrwOO9dgzAzswEuT4F4OSIWF57E\nzMyaSp4CsVzSAuAOklNMgLu5mpkNdHkKxIdICsPRdevczdXMbIDLPR9EFTzUhg0YHmrDSlT4UBt1\nO7qOdLrRehFxVl93bmZmzSvPKaYf1y1vC5wEvFhMHDMzaxY9PsUkqQVYFhGfKybS+/blU0w2MPgU\nk5WozPkgOvsY0JrnjZJ2kXSvpCclPS7pvHT9KElLJa2UtETSyF7kMDOzAuWZUa5jXogOa4CLIuLW\nbjcujQPGRcQjkrYHHgJOBM4EXo2Iv5V0ITAqImZmfN4tCBsY3IKwEvVXC6LUXkySFgL/kD4Oj4j2\ntIi0RcTeGe93gbCBwQXCSlR4LyZJu3X1wYhY3ZMdSZoI7A/8OzA2ItrT7ayRlOuUlZmZlaerXkx3\n8t6Uox0CGENyDWJI3p2kp5duAc6PiA2SOn+VavjVavbs2ZuXa7UatVot727NzAaFtrY22tra+n27\nuU8xpS2AC4GjgO9HxN/n/NxQkq6yd0XElem6FUCt7hTTfRGxT8ZnfYrJBgafYrISldaLSdLHJF0P\n3EVykfnjeYtD6ofAUx3FIbUYOCNdPh1Y1IPtmZlZCRq2ICR9ErgE+ATwt8ANEfFujzYuHQzcTzJU\neKSPi4EHgJuAXYFVwLSIWJfxebcgbGBwC8JKVHgvJknvAs+RXIv4QGGIiPP6uvPuuEDYgOECYSUq\nYywmj7VkZjaIeTRXszK4BWElqnKoDTMzGwRcIMzMLJMLhJmZZcpzH8Sekn4q6Yn0+X6SLi0+mpmZ\nVSlPC+Ia4CJgI0BEPAacWmQoMzOrXp4CMSwiHui07p0iwpiZWfPIUyBekfRR0gH1JJ0MvFRoKjMz\nq1yeCYN2B64GPge8DjwDnBYRzxYezvdB2EDh+yCsRKVPGCRpO6AlIt7o607zcoGwAcMFwkpUxlAb\nHTvaBvgLYCIwVEr2GRHf6uvOzcyseXVbIEiG4v5PkqG+3y42jpmZNYs8BWKXiDim8CRmZtZU8vRi\n+oWkfQtPYmZmTaWr+SCeADaRtDI+BjxNcopJQETEfoWH80VqGyh8kdpKVMZF6p2B/fu6AzMz2zJ1\nVSCeiYhVpSUxM7Om0lWBaJV0QaMXI+LyAvKYmVmT6KpADAG2J7nmYGZmg0xXF6kfjohJJefpnMEX\nqW1g8EVqK1EZU4665WBmNoh11YLYISJeKzlP5wxuQdjA4BaElaj0wfqq4AJhA4YLhJWojFNMZmY2\niLlAmJlZJhcIMzPL5AJhZmaZCi0Qkq6V1C7psbp1oyQtlbRS0hJJI4vMYGZmvVN0C+I64Aud1s0E\n7omIvYB7gYsKzmBmZr1QaIGIiGXA651WnwjMTZfnAlOLzGBmZr1TxTWI1ohoB4iINUBrBRnMzKwb\nzXCR2ncPmZk1oTxzUve3dkljI6Jd0jhgbVdvnj179ublWq1GrVYrNp2Z2Ramra2Ntra2ft9u4UNt\nSJoI3BER+6bPLwNei4jLJF0IjIqImQ0+66E2bGDwUBtWoi1iLCZJC4AaMBpoB2YBC4GbgV2BVcC0\niFjX4PMuEDYwuEBYibaIAtFXLhA2YLhAWIk8WJ+ZmRXKBcLMzDK5QJiZWSYXCDMzy+QCYWZmmVwg\nzMwskwuEmZllcoEwM7NMLhBmZpbJBcLMzDK5QJiZWSYXCDMzy+QCYWZmmVwgzMwskwuEmZllcoEw\nM7NMLhBmZpbJBcLMzDK5QJiZWSYXCDMzy+QCYWZmmVwgzMwskwuEmZllcoEwK0NE1QnMeswFwszM\nMrlAmJlZJhcIMzPL5AJhZmaZKisQko6R9GtJv5F0YVU5zMwsWyUFQlIL8A/AF4BPANMl7V1Flp5q\na2urOsIHNGMmaM5czpSPM+XXrLn6Q1UtiAOA30bEqojYCPwIOLGiLD3SjAdDM2aC5szlTPk4U37N\nmqs/VFUgdgaeq3v+fLrOzMyahC9Sm5lZJkUFd3hKOgiYHRHHpM9nAhERl3V6n28/NTPrhYhQX7dR\nVYEYAqwEjgReAh4ApkfEitLDmJlZpqFV7DQi3pX0P4ClJKe5rnVxMDNrLpW0IMzMrPlVdR/EtZLa\nJT3W4PXDJa2T9HD6uLTT6y3p+sXNkEnSSEk3S1oh6UlJBzZBpq9LekLSY5LmS9q6jEzpe2qSlqf7\nv69ufWE3R/Y2l6RdJN2b/r09Lum8qjPVvVb6cd5VpqqO824yVXKcS/pGmufh9Lh5R9KH09cqO84b\n5er1cR4RpT+AQ4D9gccavH44sLiLz38d+Neu3lNmJuB64Mx0eSgwospMwE7A08DW6fMbgb8sKdNI\n4Elg5/T5junPFuB3wARgK+ARYO8S//4a5RoH7J8ub09ybaxfcvU2U93rVRznDTNVeJw3+rur7Djv\n9N4/B+5Jlys9zrvI1avjvJIWREQsA17v5m2ZV+Al7QIcB/ygGTJJGgEcGhHXpdt5JyLWV5kpNQTY\nTtJQYBjwYkmZvgzcGhEvpO9/JV1f6M2Rvc0VEWsi4pF0eQOwgn66J6cPv6sqj/PMTBUf5w1/T1R3\nnNebDtyQLld9nGfm6u1x3sz3QUyR9IikOyV9vG793wF/DVRx8SQr00eAVyRdlzbrrpb0oSozRcSL\nwP8BVgMvAOsi4p6S8uwJ7CDpPkm/kvTVdH3VN0c2yrWZpIkk387+owkyVXWcN8pU5XGemani4xyA\n9HdwDHBruqrq47xRrvrXJpLzOG/WAvEQsFtE7E8yZtNCAEl/DrSnlVA0/vZcWiaSpvYk4KqImAS8\nCcysMlN6LvREkmbuTsD2kr5cUqaO38exJAfoNyXtUdK+u9JlLknbA7cA56ffsCrLJOl4qjvOG/2e\nqjzOG/2eqjzOO5wALIuIdSXvtzuZuXp6nDdlgYiIDRHxZrp8FzBU0g7A54AvSnqapOl0hKR5FWXa\nKs30PPBcRDyYvvUWkoO5ykxHAU9HxGsR8S5wG8nvrgzPA0si4o8R8SpwP/Apkm94u9W9b5d0XVka\n5SI9PXEL8H8jYlETZDqYio7zLjJVdpx3kanK47zDqbx3egmqP847dM7Vq+O8ygLR8JuRpLF1ywcA\nLelBcHFE7BYRu5P8Au6NiL+sKJPSTO3Ac5L2TF8+EniqykwkTe6DJG0rSWmm/rzPpKtvtYuAQyQN\nkTQMODDd96+APSRNSHuanAr0W++cPuQC+CHwVERc2c95epWpyuO8i0yVHeeNMlHtcY6kkSQdRer/\ns636OG+UC3pxnFdyo5ykBUANGC1pNTAL2JpkuI2rgZMl/RWwEXgL+C9Nnuk8YL6krUh6VZxZZaaI\neEDSLcDy9LXlwNVlZIqIX0taAjwGvAtcHRFPpZ8t7ObI3uaSdDDwFeBxSctJzvlfHBF3V5Wpr/st\nMFMlx3k3x1Qlx3n6tqkkLZu3Oj4XBd8E3NtcvT3OfaOcmZllasprEGZmVj0XCDMzy+QCYWZmmVwg\nzMwskwuEmVkvKMcggz3Y1qck/ULJQHqPSJpW99qRkh5SMgjf/ZJ27/TZyZI2SvpSX3N8IJd7MZmZ\n9ZykQ4ANwLyI2K+P29qDpKvq7yWNJxklYe+IWC9pJXBCRPwm7dY+OSLOSj/XAvyEpJv7DyPitr7k\n6KyS+yDMmk16B/pPSfqHjyfpb7+W5IakP0TEIRXGsyYUEcskTahfl367vwrYkWQ4krMj4jc5tvW7\nuuWXJK0FxgDrgU0kI9qS/qwfkPBckrujJ/fhj9KQC4QZkN6B/mkASX8DbIiIy6tNZVugq4Fz0pbA\nAcA/kdzhnVv6ua0i4vfpqrOBuyS9SVIwDkrftxMwNSKOSD/T71wgzD7ofcMYSHojIoZLOhyYA6wD\nPgncDDwOnA9sS/KP9RlJOwL/DOyabuLrEfGL0tJbJSRtRzIW1M3p0B+QzAmBpJOAb/H+0XkFPB8R\nx9ZtYzwwD6gf2ffrwDER8aCk/0ky0u/ZwBXAhZ22169cIMy6V/+Pej9gb5Ii8TRwTUQcqGSGrnOB\nC4Argcsj4heSdgWWAB/HBroW4PV0tNv3iYjbgdu7+rCk4cCPgYsi4lfpuh2BT9UNkngTcFe6/Fng\nR2kx2hE4VtLGiOi3sZ9cIMx65lcRsRZA0u9JxtyBpCVRS5ePAvap+xa5vaRhHSPv2oCyeeC8iHhD\n0jOSTo6IWwAk7RcR3fZySse3WgjMTYtJh9eBEZL2SK9THE06IGE6mGPH568D7ujP4gAuEGY99Xbd\n8qa655t479+TgAMjmVHMBqgGA+d9BfhnJfPDDyWZUS5PN9hpJNOJjpJ0Jkmr9YyIeEzS2cBtkt4l\nKRhnZXy+kO6oLhBm3evpud2lJNclvgdJH/eIeLTfU1mlIqLR5ETHNljf1bbmA/MbvLaIDw7d3fk9\nWUWjz3yjnFn3Gn07a7T+fOCzkh6V9ARwTjGxzIrlG+XMzCyTWxBmZpbJBcLMzDK5QJiZWSYXCDMz\ny+QCYWZmmVwgzMwskwuEmZllcoEwM7NM/x/lLmP74ddUggAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x5bf5190>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "run_simulation(10.0, model=m2, y0={'A': 60, 'B': 60}, solver='meso')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Structure (e.g. membrane, cytoplasm and nucleus) is only supported by `spatiocyte` and `meso` now. For the simulation, `location` that each species belongs to must be specified in its attribute first."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "with species_attributes():\n",
    "    A | {'D': '1', 'location': 'S'}  # 'S' is a name of the structure\n",
    "\n",
    "m3 = get_model()  # with no reactions"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "E-Cell4 supports primitive shapes as a structure like `Sphere`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "sphere = Sphere(Real3(0.5, 0.5, 0.5), 0.48)  # a center position and radius"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "E-Cell4 provides various kinds of `Observer`s, which log the state during a simulation. Two observers are declared to log positions of molecules. `FixedIntervalTrajectoryObserver` logs a trajectory of a molecule, and `FixedIntervalHDF5Observer` saves `World` to a HDF5 file at the given interval:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "obs1 = FixedIntervalTrajectoryObserver(1e-3)\n",
    "obs2 = FixedIntervalHDF5Observer(0.1, 'test%02d.h5')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Then, `run_simulation` accepts structures and observers as arguments `structure` and `observers` respectively (see also `help(run_simulation)`):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "RuntimeError",
     "evalue": "save(const std::string) is not supported by this space class",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mRuntimeError\u001b[0m                              Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-27-183eb186bbd1>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      1\u001b[0m run_simulation(1.0, model=m3, y0={'A': 60}, structures={'S': sphere},\n\u001b[1;32m----> 2\u001b[1;33m                solver='spatiocyte', observers=(obs1, obs2), return_type=None)\n\u001b[0m",
      "\u001b[1;32mc:\\python35\\lib\\site-packages\\ecell4\\util\\simulation.py\u001b[0m in \u001b[0;36mrun_simulation\u001b[1;34m(t, y0, volume, model, solver, factory, is_netfree, species_list, without_reset, return_type, opt_args, opt_kwargs, structures, observers)\u001b[0m\n\u001b[0;32m    167\u001b[0m         \u001b[0mobservers\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;33m(\u001b[0m\u001b[0mobs\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m)\u001b[0m \u001b[1;33m+\u001b[0m \u001b[0mtuple\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mobservers\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    168\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 169\u001b[1;33m     \u001b[0msim\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mt\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m-\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mobservers\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    170\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    171\u001b[0m     \u001b[1;32mif\u001b[0m \u001b[0mreturn_type\u001b[0m \u001b[1;33m==\u001b[0m \u001b[1;34m'matplotlib'\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mlib\\ecell4\\spatiocyte.pyx\u001b[0m in \u001b[0;36mecell4.spatiocyte.SpatiocyteSimulator.run (lib/ecell4\\spatiocyte.cpp:11191)\u001b[1;34m()\u001b[0m\n",
      "\u001b[1;31mRuntimeError\u001b[0m: save(const std::string) is not supported by this space class"
     ]
    }
   ],
   "source": [
    "run_simulation(1.0, model=m3, y0={'A': 60}, structures={'S': sphere},\n",
    "               solver='spatiocyte', observers=(obs1, obs2), return_type=None)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "E-Cell4 also provides visualizations including an interactive visualization on IPython Notebook like `viz.plot_world`. `viz.plot_world` plots positions of molecules in 3D. In addition, by using `load_world`, you can easily restore the state of `World` from a HDF5 file:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# viz.plot_world(load_world('test00.h5'), species_list=['A'])\n",
    "viz.plot_world(load_world('test00.h5'), species_list=['A'], interactive=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Also for `FixedIntervalTrajectoryObserver`, `viz.plot_trajectory` plots trajectories in the interactive way:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# viz.plot_trajectory(obs1)\n",
    "viz.plot_trajectory(obs1, interactive=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "For more details, see [5. How to Log and Visualize Simulations](5. How to Log and Visualize Simulations.ipynb)."
   ]
  }
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