diff --git a/Example_Mesh_Creation.ipynb b/Example_Mesh_Creation.ipynb
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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Notes on Spatial Information for StochSS\n",
+    "\n",
+    "When setting up a spatial problem in StochSS information about the geometry needs to be provided through two files: a\n",
+    "file containing the mesh information in DOLFIN XML format and a text file containing information about subdomains. The\n",
+    "file with subdomain information is optional in general (if it is not provided the entire mesh will belong to one subdomain).\n",
+    "Below is a tutorial on how to provide that information in a variety of cases.\n",
+    "\n",
+    "## Mesh Library \n",
+    "\n",
+    "The first and simpilest scenario is using one of the default built­in meshes provided by StochSS in the Mesh Library.\n",
+    "These include simple example mesh and subdomain combinations that are common in biological modeling. For example\n",
+    "there is a unit sphere with a membrane (i.e. the volume is one subdomain and the surface is another), a unit cube witha\n",
+    "membrane, a cylinder with the two ends being different subdomains among others. If for a given problem these are not\n",
+    "sufficient then mesh and subdomain information can be provided by attaching files. One simple case where creating and\n",
+    "attaching a file may be necessary could involve using the DOLFIN built in meshes but with different subdomains than\n",
+    "provided in the Mesh Library. This can be done as follows.\n",
+    "## Using DOLFIN Built-In Geometry with Subdomains Outside of Mesh\n",
+    "Library\n",
+    "For example consider a sphere with three different subdomains: the top half of the membrane, the bottom half of the\n",
+    "membrane and the volume. This can be done using pyurdme as follows (pyurdme and FEniCS are software packages\n",
+    "that are automatically installed during the StochSS installation and DOLFIN is a library within FEniCS).\n",
+    "First the appropriate libraries need to be imported:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "FILENAME = \"sphere_top_bot_mesh.xml\"\n",
+    "SD_FILENAME = \"sphere_top_botsubdomains.txt\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "import dolfin\n",
+    "import mshr\n",
+    "import os\n",
+    "import pyurdme"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "class top_half_membrane(dolfin.SubDomain):\n",
+    "    def inside(self,x,on_boundary):\n",
+    "        return on_boundary and x[2]>=0\n",
+    "class bottom_half_membrane(dolfin.SubDomain):\n",
+    "    def inside(self,x,on_boundary):\n",
+    "        return on_boundary and x[2]<=0"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "class sphere_top_bot(pyurdme.URDMEModel):\n",
+    "    def __init__(self,model_name=\"polarization\"):\n",
+    "        pyurdme.URDMEModel.__init__(self,model_name)\n",
+    "        #DefineGeometry\n",
+    "        sphere=mshr.Sphere(dolfin.Point(0.0,0.0,0.0),1.0)\n",
+    "        self.mesh=pyurdme.URDMEMesh(mesh=mshr.generate_mesh(sphere,10))\n",
+    "        cell_function=dolfin.CellFunction(\"size_t\",self.mesh)\n",
+    "\n",
+    "        self.add_subdomain(top_half_membrane(),2)\n",
+    "        self.add_subdomain(bottom_half_membrane(),3)\n",
+    "        #Defineinitialpopulations\n",
+    "        self.set_initial_condition_scatter({},[1])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "model=sphere_top_bot()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "sd=model.get_subdomain_vector()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "#This is a dolfin xml file with mesh information\n",
+    "dolfin.File(FILENAME) << model.mesh"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "import base64\n",
+    "import IPython.display\n",
+    "with open(FILENAME) as fd:\n",
+    "    b64 = base64.b64encode(fd.read())\n",
+    "    payload = b64.decode()\n",
+    "    html = '<H1><a download=\"{filename}\" href=\"data:text/csv;base64,{payload}\" target=\"_blank\">{title}</a></H1>'\n",
+    "    html = html.format(payload=payload,title=\"Click here to Download Mesh\",filename=FILENAME)\n",
+    "IPython.display.HTML(html)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "#This is the file to capture information about subdomains\n",
+    "with open(SD_FILENAME,'w') as sfd:\n",
+    "    for ndx,val in enumerate(sd):\n",
+    "        sfd.write(\"{0},{1}\\n\".format(ndx,val))\n",
+    "import base64\n",
+    "import IPython.display\n",
+    "with open(SD_FILENAME) as fd:\n",
+    "    b64 = base64.b64encode(fd.read())\n",
+    "    payload = b64.decode()\n",
+    "    html = '<H1><a download=\"{filename}\" href=\"data:text/csv;base64,{payload}\" target=\"_blank\">{title}</a></H1>'\n",
+    "    html = html.format(payload=payload,title=\"Click here to Download SD file\",filename=SD_FILENAME)\n",
+    "IPython.display.HTML(html)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "#  IF you want to visualize your mesh, execute the following two cells"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "# Code to setup javascript display libraries\n",
+    "import os.path\n",
+    "import IPython.display\n",
+    "with open(os.path.join(os.path.dirname(pyurdme.__file__),'data/three.js_templates/js/three.js')) as fd:\n",
+    "    bufa = fd.read()\n",
+    "with open(os.path.join(os.path.dirname(pyurdme.__file__),'data/three.js_templates/js/render.js')) as fd:\n",
+    "    bufb = fd.read()\n",
+    "with open(os.path.join(os.path.dirname(pyurdme.__file__),'data/three.js_templates/js/OrbitControls.js')) as fd:\n",
+    "    bufc = fd.read()\n",
+    "IPython.display.display(IPython.display.HTML('<script>'+bufa+bufc+bufb+'</script>'))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "model.mesh"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": []
+  },
+  {
+   "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": 1
+}