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kaizu/Example.ipynb

Created April 7, 2015 09:31
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Example.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from ecell4 import *"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"m = NetworkModel()\n",
"m.add_species_attribute(Species(\"A\", \"0.005\", \"1\")) # name, radius, D\n",
"m.add_species_attribute(Species(\"B\", \"0.005\", \"1\"))"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"w = lattice.LatticeWorld(Real3(1, 1, 1), 0.005) # edge_lengths, voxel_radius\n",
"w.bind_to(m)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"w.add_molecules(Species(\"A\"), 120)\n",
"w.add_molecules(Species(\"B\"), 120)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<html>\n",
" <head>\n",
" <script type=\"text/javascript\">\n",
" (function(){\n",
" if(window[\"THREE\"] === undefined || window[\"d3\"] === undefined){\n",
"\t require.config({\n",
"\t paths:{\n",
"\t d3: [\n",
"\t 'https://cdnjs.cloudflare.com/ajax/libs/d3/3.4.4/d3.min',\n",
"\t 'custom/d3.min'\n",
"\t ],\n",
"\t THREE: [\n",
"\t 'https://cdnjs.cloudflare.com/ajax/libs/three.js/r66/three.min',\n",
"\t 'custom/three.min'\n",
"\t ],\n",
" Elegans: [\n",
"\t 'https://rawgit.com/domitry/elegans/master/release/elegans',\n",
"\t 'custom/elegans'\n",
"\t ]\n",
"\t },\n",
"\t shim:{\n",
"\t THREE: {\n",
"\t exports: 'THREE'\n",
"\t },\n",
"\t Elegans: {\n",
"\t deps: ['THREE'],\n",
"\t exports: 'Elegans'\n",
"\t }\n",
"\t }\n",
"\t });\n",
"\n",
"\t require([\"d3\", \"THREE\"], function(d3){\n",
"\t window[\"d3\"] = d3;\n",
"\t });\n",
" }\n",
"\n",
" require([\"Elegans\"], function(){\n",
"\t console.log(\"Begin rendering...\");\n",
"\t var model = {\"plots\": [{\"data\": {\"y\": [0.9526279441628825, 0.40125843708678993, 0.7736493607140986, 0.9786087062764157, 0.6062177826491071, 0.42723919920032305, 0.35795716689756796, 0.5888972745734182, 0.4416729559300637, 0.89489291724392, 0.40125843708678993, 0.2540341184434353, 0.2598076211353316, 0.18475208614068023, 0.11258330249197702, 0.3204293994002423, 0.2800148805569685, 0.874685657822283, 0.6697263122599659, 0.0808290376865476, 0.7649891066762542, 0.046188021535170064, 0.9612881982007269, 0.5455960043841963, 0.4792007234273894, 0.9035531712817644, 0.40125843708678993, 0.5744635178436777, 0.9786087062764157, 0.6437455501464328, 0.29733538863265724, 0.48497422611928565, 0.16743157806499148, 0.7130275824491878, 0.9093266739736606, 0.8169506309033205, 0.7476685986005654, 0.5715767664977295, 0.16454482671904336, 0.6610660582221216, 0.2107328482542134, 0.028867513459481287, 0.7649891066762542, 0.15877132402714708, 0.5744635178436777, 0.1905255888325765, 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\"Particles\", \"options\": {\"color\": \"#1f78b4\", \"name\": \"B\", \"size\": 0.15}}], \"options\": {\"width\": 500, \"range\": {\"y\": [0.0, 1.0], \"x\": [0.0, 1.0], \"z\": [0.0, 1.0]}, \"grid\": true, \"autorange\": false, \"height\": 500}};\n",
"\t Elegans.Embed.parse(\"#\"+\"viz609342fa-ae39-4626-a8d6-1a19341b30ac\",model).render();\n",
" });\n",
" })();\n",
" </script>\n",
" </head>\n",
" <body>\n",
" <div id=\"viz609342fa-ae39-4626-a8d6-1a19341b30ac\"></div>\n",
" </body>\n",
"</html>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"cfg = viz.plot_world(w)"
]
},
{
"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
}
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