Introduction.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "slideshow": {
     "slide_type": "skip"
    }
   },
   "outputs": [],
   "source": [
    "from IPython.display import IFrame, HTML\n",
    "# from traitlets.config.manager import BaseJSONConfigManager\n",
    "# path = \"/Users/chungheng/anaconda3/envs/py3/etc/jupyter/nbconfig\"\n",
    "# cm = BaseJSONConfigManager(config_dir=path)\n",
    "# cm.update(\"livereveal\", {\n",
    "#             \"width\": 1024,\n",
    "#             \"height\": 768,\n",
    "#             \"theme\": \"solarized\",\n",
    "#             \"transition\": \"zoom\",\n",
    "#             \"start_slideshow_at\": \"beginning\",\n",
    "# })"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "# Fruit Fly Brain Hackathon\n",
    "\n",
    "<div><img src='background.jpeg'></div>\n",
    "\n",
    "**Wednesday, March 20, 2019** <br>\n",
    "**Center for Neural Engineering and Computation** <br>\n",
    "**Columbia University, New York, NY, USA** <br>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "notes"
    }
   },
   "source": [
    "Welcome to the forth fruit fly brain hackathon! My name is Chung-Heng, and I am one of the Hackathon organizers together with yiyin, mehmet and Tingkai.\n",
    "\n",
    "I will give a brief introduction, and talk about the schedule.\n",
    "\n",
    "We are a group people interested in how brain works, and we \n",
    "champion the focus on emulating the fruit fly brain for understanding brain functions.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Why *Fly*?\n",
    "\n",
    "<br>\n",
    "<div class=\"row\">\n",
    "  <div class=\"col-md-8\">\n",
    "     <ul>\n",
    "      <li>Rich data, ex. genetic information, anatomy, physiology, <i>etc</i>.</li>\n",
    "      <li>Building blocks of cognition.</li>\n",
    "      <li>100k neurons - can be emulated on the commodity hardware.</li>\n",
    "      <li>Neurodegenerative diseases.</li>\n",
    "    </ul>\n",
    "  </div>\n",
    "  <div class=\"col-md-4\"  markdown=\"1\">\n",
    "    <img width=\"400px\" src=\"ffbo.gif\">\n",
    "  </div>\n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "\n",
    "<div class=\"row\" style=\"display: none\">\n",
    "  <div class=\"col-sm-1\">\n",
    "  </div>\n",
    "  <div class=\"col-sm-1\">\n",
    "    <img width=\"200px\" style=\"background: #000\" src=\"https://www.embedded-vision.com/sites/default/files/news/GoogleAI_logo_horizontal_color_rgb.png\">\n",
    "  </div>\n",
    "  <div class=\"col-sm-1\">\n",
    "    <img width=\"200px\" style=\"background: #000; margin-top:30%\" src=\"https://www.janelia.org/sites/all/themes/janelia7/logo.png\">\n",
    "  </div>\n",
    "  <div class=\"col-sm-1\">\n",
    "    <img width=\"100px\" style=\"background: #000; margin-top:15%\" src=\"https://dl4physicalsciences.github.io/images/NIPS.svg\">\n",
    "  </div>\n",
    "</div>\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "*\"Everything should be as simple as possible, but not simpler.\"*\n",
    "<p style='text-align: right;'> by Albert Einstein </p>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "notes"
    }
   },
   "source": [
    "It is a golden era for the fly community.\n",
    "There are massive amount of data for fly generated in the recent years.\n",
    "The data acuqistion has been broght up to industrial scale.\n",
    "\n",
    "The fly demonstrates brain functions that are building blocks of cognition.\n",
    "For example, the fly generates an internal representation of the external world.\n",
    "\n",
    "Fly has only 100 thousands of neurons which allows to simulate the fly brain on\n",
    "modern hardwares.\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Fruit Fly Brain Observatory\n",
    "\n",
    "A collaborative ecosystem for *All*:\n",
    "<div class=\"row\">\n",
    "  <div class=\"col-md-6\">\n",
    "    <div>\n",
    "    <ul>\n",
    "      <li>neurobiologists</li>\n",
    "      <li>modelers</li>\n",
    "      <li>hackers</li>\n",
    "    </ul>\n",
    "    </div>\n",
    "    <br>\n",
    "    <div style=\"visibility:hidden\">\n",
    "      FFBO provides <span style='color:#f442d4'>integration</span> of:\n",
    "      <ul>\n",
    "        <li>neurogenetics, anatomy and physiology</li>\n",
    "        <li>computational modeling data</li>\n",
    "        <li>executable code</li>\n",
    "      </ul>  \n",
    "    </div>\n",
    "  </div>\n",
    "  <div class=\"col-md-6 col-offset-6\"  markdown=\"1\">\n",
    "    <img src=\"ffbh.png\" style=\"background: #000\" alt=\"drawing\"height=\"600px\" class=\"center-block\"/>\n",
    "  </div>\n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## Fruit Fly Brain Observatory\n",
    "\n",
    "A collaborative ecosystem for *All*:\n",
    "<div class=\"row\">\n",
    "  <div class=\"col-md-6\">\n",
    "    <div>\n",
    "    <ul>\n",
    "      <li>neurobiologists</li>\n",
    "      <li>modelers</li>\n",
    "      <li>hackers</li>\n",
    "    </ul>\n",
    "    </div>\n",
    "    <br>\n",
    "    <div>\n",
    "      FFBO provides <span style='color:#f442d4'>integration</span> of:\n",
    "      <ul>\n",
    "        <li>neurogenetics, anatomy and physiology</li>\n",
    "        <li>computational modeling data</li>\n",
    "        <li>executable code</li>\n",
    "      </ul>  \n",
    "    </div>\n",
    "  </div>\n",
    "  <div class=\"col-md-6 col-offset-6\"  markdown=\"1\">\n",
    "    <img src=\"ffbh.png\" style=\"background: #000\" alt=\"drawing\"height=\"600px\" class=\"center-block\"/></div>\n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "notes"
    }
   },
   "source": [
    "We launch the fruit fly brain observatory or FFBO. The goal of ffbo is to create a meeting ground for researchers of different experties, ex. cs, biologists, modelers, to study the functions of the fly brains. FFBO integrates code, models, and data, and make them accessable for users."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## NeuroNLP\n",
    "*A Natural Language Portal for Aggregated Fly Brain Data.*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "scrolled": false,
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <iframe\n",
       "            width=\"100%\"\n",
       "            height=\"600px\"\n",
       "            src=\"https://neuronlp.fruitflybrain.org/\"\n",
       "            frameborder=\"0\"\n",
       "            allowfullscreen\n",
       "        ></iframe>\n",
       "        "
      ],
      "text/plain": [
       "<IPython.lib.display.IFrame at 0x1046d4898>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "IFrame('https://neuronlp.fruitflybrain.org/', width='100%', height='600px')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## NeuroGFX\n",
    "*A Graphic Functional Explorer for the Fruit Fly Brain*."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": true,
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "        <iframe\n",
       "            width=\"100%\"\n",
       "            height=\"500px\"\n",
       "            src=\"https://neurogfx.fruitflybrain.org/\"\n",
       "            frameborder=\"0\"\n",
       "            allowfullscreen\n",
       "        ></iframe>\n",
       "        "
      ],
      "text/plain": [
       "<IPython.lib.display.IFrame at 0x10458fe10>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "IFrame('https://neurogfx.fruitflybrain.org/', width='100%', height='500px')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## FlyBrainLab + Hackathon\n",
    "*<span style='color:#f442d4'>Integration</span>&nbsp; - &nbsp;<span style='color:#b241f4'>Interaction</span>&nbsp; - &nbsp;<span style='color:#5261f4'>Innovation</span>*\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "&#128077; FFBO spearheads an <i style='color:#f442d4'>integrative</i> ecosystem. <p style='text-align: right;'> <i>... still barriers between different domains.</i></p>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "### &#x270C; FlyBrainLab enables <i style='color:#b241f4'>interactive</i> computing ... <i>JupyterLab came out in 2018.</i>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "### &#128293; Hackathon sparks <i style='color:#5261f4'> innovative</i> ideas! ... It is <strong>YOUR</strong> turn now.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Schedule\n",
    "\n",
    "* 09:00 - 09:10 - Introduction to the Fruit Fly Brain Hackathon.\n",
    "* 09:10 - 09:15 - Self-introductions by Participants. \n",
    "* 09:15 - 09:30 - Introduction to FlyBrainLab.\n",
    "* 09:30 - 12:30 - Hacking: Basic Features of FBL.\n",
    "* 12:30 - 13:30 - Lunch Break.\n",
    "* 13:30 - 13:45 - Building Models of Fly Brain Neuropil Using FBL.\n",
    "* 13:45 - 13:00 - Discussions and Summary of Project Ideas.\n",
    "* 14:00 - 18:00 - Hacking."
   ]
  }
 ],
 "metadata": {
  "celltoolbar": "Slideshow",
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.6.6"
  },
  "livereveal": {
   "footer": "<div style='width: 100vw; margin: 0 auto;'><h5 style='text-align:center;'>Fruit Fly Brain Hackathon 2019</h5></div>",
   "start_slideshow_at": "beginning",
   "theme": "serif",
   "transition": "none"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}