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<!DOCTYPE html>
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<meta name="Distribution" content="Global" />
<meta name="Author" content="Jean-Christophe Taveau" />
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<h1 id="project_title">Crazybiocomputing.GitHub.io</h1>
<h2 id="project_tagline">Tools about Bioinformatics: Mowgli & ????</h2>
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<h2>A- Molecular Structure Visualization</h2>
  <h3>1- Protein Data Bank</h3>
    <h4>1-1- wwPDB</h4>
  <p>The main website of the Protein Data Bank (PDB) is <a href="http://www.wwpdb.org/">wwPDB</a>
  and contains all the documentation about the validation and deposition of an atomic 3D structure.</p>
  <p>In this documentation, three different file formats are used in PDB as detailed <a href="http://www.wwpdb.org/documentation/file-format">here</a>.
  <ol>
   <li>PDBx/mmCIF</li>
   <li>PDBML/XML</li>
   <li>PDB</li>
  </ol>
  <p>Among them, we are only interested in the <a href="http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html">PDB file format</a>.</p>
    <h4>1-2- PDB File format</h4>

  <h3>2- Display Modes</h3>
    <p>By default, a PDB viewer offers various rendering modes as listed below...</p>
    <blockquote><b>Note:</b> The names of the rendering modes correspond to those of Rasmol and they can vary depending of the app.</blockquote>
    <h4>2-1- Atoms Rendering modes</h4>
      <h5>2-1-1- Spacefill</h5>
      <p>In Spacefill mode, all the atoms are displayed as spheres whose radii correspond to the radii of the corresponding
      spheres of Van der Waals. </p>
      <h5>2-1-2- Dots</h5>
      <p>In this mode &mdash; identical to the Spacefill &mdash; the surfaces of the spheres are covered by equidistant dots
      leading to a transparent rendering of the spheres. Thus, the Dots mode can be combined with another mode.</p>
    <h4>2-2- Bonds Rendering modes</h4>
      <h5>2-2-1- Wireframe</h5>
      <p>All the bonds are displayed as lines. The atoms are thus, located at the ends of the segments. </p>
      <h5>2-2-2- Sticks</h5>
      <p>This mode is identical to the wireframe mode but the lines which are replaced by cylinders (aka sticks).</p>
    <h4>2-3- Hybrid Rendering modes</h4>
      <h5>2-3-1- Ball & Sticks</h5>
      <p>This is a combination of Spacefill and Sticks. However, the radii of the spheres are smaller and
      of constant size regardless of the nature of the atoms.</p>
    <h4>2-4- Secondary Structures Rendering modes</h4>
      <h5>2-4-1- Backbone</h5>
      <h5>2-4-1- Trace</h5>
      <h5>2-4-1- Strands</h5>
      <h5>2-4-2- Ribbons</h5>
      <h5>2-4-3- Cartoon</h5>

<h2>B- Mini-courses about EMDB</h2>

<h3>00: Electron Microscopy Data Bank</h3>
<p>By Jean-Christophe Taveau</p>

<h3>0: Git, github, and grunt</h3>
<p>By Aurore P., Jeremy T. [prom 2016]</p>
  <ul>
  <li>Advanced use of git</li>
  <li>Tools of github (fork, pull request, web page, newsgroups, etc.)</li>
  <li>App packaging: grunt and main plugins</li>
  </ul>

<h3>1: 3D reconstruction using single particle electron microscopy </h3>
<p>By Khoudia F., Anne M.</p>
  <ul>
  <li>Principle</li>
  <li>Methods and softwares</li>
  </ul>

<h3>2: Data compression (gzip/ gunzip)</h3>
<p>By Jean-David A., Anh T.T.</p>
  <ul>
  <li>Presentation of the compression algorithms</li>
  <li>Libraries in JavaScript and how to use them for EMDB Data</li>
  </ul>
<h3>3: MRC File format</h3>
<p>By Quentin J., Myriam L.</p>
  <ul>
  <li>Presentation of the contents of header and data (pixels, voxels)</li>
  <li>Synopsis how to read such file with JavaScript</li>
  </ul>
<h3>4: SPIDER File format</h3>
<p>By Aurélien B., Emeline D.</p>
  <ul>
  <li>Presentation of the contents of header and data (pixels, voxels)</li>
  <li>Synopsis how to read such file with JavaScript</li>
  </ul>
<h3>5: TIFF File format</h3>
<p>By Rudy A., Anthime S.</p>
  <ul>
  <li>Presentation of the contents of header and data</li>
  </ul>
<h3>6: Isosurfaces and Marching Cubes</h3>
<p>By Noémie O.D.A., Estelle A.</p>
  <ul>
  <li>Presentation of the algorithms and variants</li>
  <li>Implementation in WebGL</li>
  </ul>
<h3>7: Direct Volume Renderning</h3>
<p>By Pierre B., Kevin J.</p>
  <ul>
  <li>Presentation of the various algorithms</li>
  <li>Implementation in WebGL</li>
  </ul>

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