elegans/index.html at master · buhrmann/elegans · GitHub

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<!DOCTYPE html>
<html lang="en">
  <head>
    <meta charset="utf-8">
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <meta
      name="description"
      content="A C. elegans connectome explorer and neural network visualization"
    >
    <title>Worm Circuitry Explorer</title>
    <link rel="shortcut icon" href="/static/images/worm-32.png">
    <link rel="stylesheet" href="/static/css/bootstrap.min.css">
    <link rel="stylesheet" href="/static/css/d3.css">
    <link rel="stylesheet" href="/src/styles/app.css">
  </head>
  <body class="graph-page">
    <main id="app-shell">
      <p class="status-banner hidden" id="graph-status" role="status"></p>
      <div id="graph"></div>

      <div class="topwrapper out" id="intro-panel">
        <div class="introheader">
          <div class="introheader-title">
            <h3>Worm Circuitry Explorer</h3>
            <button
              type="button"
              class="intro-close"
              id="intro-handle"
              aria-label="Close intro panel"
            >
              <span class="glyphicon glyphicon-remove"></span>
            </button>
          </div>
          <p>
            The Worm Circuitry Explorer allows interactive exploration of the
            <em>C. elegans</em> connectome.
          </p>

          <h4>Usage</h4>
          <dl class="dl-horizontal">
            <dt>Hover</dt>
            <dd>Highlights a neuron's immediate neighborhood.</dd>
            <dt>Click</dt>
            <dd>
              Selects a node and pins its metadata in the panel on the right.
            </dd>
            <dt>Drag</dt>
            <dd>Moves and pins a node to a fixed position.</dd>
            <dt>Dbl-click</dt>
            <dd>Releases a pinned node.</dd>
          </dl>
          <h5>Subcircuits</h5>
          <p>
            Choose source and target neuron groups, constrain path length and
            connection thresholds, then fetch the subgraph connecting them.
            Expand adds back all direct connections among the fetched neurons.
          </p>
          <p class="intro-actions">
            <button type="button" class="btn btn-success" id="intro-toggle">
              Start Now
            </button>
          </p>
          <div class="intro-about">
            <h4>About</h4>
            <p>
              <a href="https://en.wikipedia.org/wiki/Caenorhabditis_elegans"><em
                >Caenorhabditis elegans</em></a>
              is a nematode worm of particular interest to many researchers as
              it was the first multicellular organism to have its whole genome
              sequenced, and remains the only organism whose connectome has
              been completed in its entirety.
            </p>
            <p>
              The Worm Circuitry Explorer allows visual and interactive
              exploration of this connectome. Its main purpose is to help
              researchers and modelers inspect subcircuits that may underlie
              particular worm behaviors.
            </p>

            <h5>Data Sources</h5>
            <p>
              The explorer covers the connectivity between the 279 somatic
              neurons whose interconnections are best established. The core
              connectivity is based on Chen et al. (2006) and Varshney et al.
              (2011), supplemented with position data from the Dynamic
              Connectome project, neuron classes from WormWeb, and sensory
              annotations maintained locally in this repository.
            </p>

            <h5>Visualization</h5>
            <p>
              The graph is rendered with modern D3 in the browser. Nodes can be
              selected to inspect metadata, dragged to pin positions, filtered
              by degree and connection thresholds, and exported in multiple
              graph formats.
            </p>

            <h5>References</h5>
            <ol class="bib">
              <li>
                Nikhil Bhatla, <a href="http://wormweb.org/">WormWeb.org</a>
              </li>
              <li>
                Chen, Hall, and Chklovskii (2006). <em>Wiring optimization can
                  relate neuronal structure and function.</em>
                PNAS 103: 4723-4728.
              </li>
              <li>
                Choe, McCormick, and Koh (2004). <em>Network connectivity
                  analysis on the temporally augmented C. elegans web: A pilot
                  study.</em>
              </li>
              <li>
                Varshney, Chen, Paniagua, Hall and Chklovskii (2011). <em
                >Structural properties of the C. elegans neuronal network.</em>
              </li>
              <li>WormAtlas, Altun et al., 2002-2015.</li>
            </ol>
          </div>
        </div>
        <button
          class="uihandle uihandle-top"
          id="intro-handle-tab"
          type="button"
          aria-label="Open intro panel"
        >
          <span class="glyphicon glyphicon-info-sign"></span>
        </button>
      </div>

      <aside class="uiwidget uiwidget-left out" id="left-widget">
        <button
          type="button"
          class="uihandle uihandle-edge uihandle-left"
          id="left-handle"
          aria-controls="left-widget"
          aria-expanded="false"
          aria-label="Toggle controls sidebar"
        >
          <span class="glyphicon glyphicon-chevron-right"></span>
        </button>

        <div class="uiwidget-body">
          <section class="formpanel formpanel-static">
            <div class="formpanel-heading">
              <span class="formpanel-title">Find neuron</span>
            </div>
            <div class="panel-body">
              <div class="input-group input-group-sm">
                <input
                  id="search-node"
                  list="search-node-options"
                  type="text"
                  placeholder="Neuron name"
                  class="form-control"
                >
                <span class="input-group-btn">
                  <button
                    type="button"
                    id="search-button"
                    class="btn btn-default"
                  >
                    Search
                  </button>
                </span>
              </div>
              <datalist id="search-node-options"></datalist>
            </div>
          </section>

          <div class="uiwidget-scroll">
            <details class="formpanel" open>
              <summary>Subgraph</summary>
              <div class="panel-body">
                <p>
                  Choose two sets of neuron groups and fetch the connecting
                  subgraph.
                </p>

                <div class="form-group token-input-group">
                  <label for="group1">Source groups</label>
                  <input
                    id="group1"
                    type="search"
                    value="ASE"
                    class="form-control input-sm"
                  >
                </div>

                <div class="form-group">
                  <label for="path-direction">Direction</label>
                  <select id="path-direction" class="form-control input-sm">
                    <option value="uni">Directed</option>
                    <option value="bi">Bidirectional</option>
                  </select>
                </div>

                <div class="form-group token-input-group">
                  <label for="group2">Target groups</label>
                  <input
                    id="group2"
                    type="search"
                    value="SMB"
                    class="form-control input-sm"
                  >
                </div>

                <div class="form-group token-input-group">
                  <label for="rec-sel">Include receptors</label>
                  <input
                    id="rec-sel"
                    type="search"
                    class="form-control input-sm"
                  >
                </div>

                <div class="form-group">
                  <label>Include muscles</label>
                  <div>
                    <label class="checkbox-inline"><input
                        type="checkbox"
                        id="mhead-check"
                      >Head</label>
                    <label class="checkbox-inline"><input
                        type="checkbox"
                        id="mneck-check"
                      >Neck</label>
                    <label class="checkbox-inline"><input
                        type="checkbox"
                        id="mbody-check"
                      >Body</label>
                  </div>
                </div>

                <div class="form-group">
                  <label for="subwslider">Minimum chemical contacts</label>
                  <output for="subwslider" id="subwlabel">1</output>
                  <input
                    type="range"
                    id="subwslider"
                    value="1"
                    min="1"
                    max="10"
                  >
                </div>

                <div class="form-group">
                  <label for="subjslider">Minimum electrical contacts</label>
                  <output for="subjslider" id="subjlabel">1</output>
                  <input
                    type="range"
                    id="subjslider"
                    value="1"
                    min="1"
                    max="10"
                  >
                </div>

                <div class="form-group">
                  <label for="subpslider">Maximum path length</label>
                  <output for="subpslider" id="subplabel">3</output>
                  <input type="range" id="subpslider" value="3" min="1" max="4">
                </div>

                <div class="form-group">
                  <label for="preset-select">Presets</label>
                  <select id="preset-select" class="form-control input-sm">
                    <option value="">Choose a preset</option>
                  </select>
                </div>

                <div
                  class="btn-group btn-group-justified btn-group-sm"
                  role="group"
                >
                  <a href="#" id="fetchbutton" class="btn btn-default">Fetch</a>
                  <a href="#" id="expandbutton" class="btn btn-default disabled"
                  >Expand</a>
                  <a href="#" id="resetbutton" class="btn btn-default">Reset</a>
                </div>
              </div>
            </details>

            <details class="formpanel">
              <summary>PubMed</summary>
              <div class="panel-body">
                <p>
                  Filter neuron groups by PubMed citation count for a query
                  term.
                </p>
                <div class="form-group">
                  <input
                    id="pmsearch"
                    type="search"
                    placeholder="chemotaxis"
                    class="form-control input-sm"
                  >
                </div>
                <div class="form-group">
                  <label for="pubnumslider">Minimum citations</label>
                  <output for="pubnumslider" id="pubnumlabel">2</output>
                  <input
                    type="range"
                    id="pubnumslider"
                    value="2"
                    min="1"
                    max="20"
                  >
                </div>
                <div class="checkbox">
                  <label><input type="checkbox" id="pubmed-check">Populate
                    only</label>
                </div>
                <button
                  type="button"
                  id="pmbutton"
                  class="btn btn-default btn-sm btn-block"
                >
                  Search PubMed
                </button>
                <p class="status-text" id="pubmed-status" role="status"></p>
              </div>
            </details>

            <details class="formpanel">
              <summary>Visibility</summary>
              <div class="panel-body">
                <div
                  class="btn-group btn-group-xs btn-group-justified"
                  role="group"
                >
                  <label class="btn btn-default active">
                    <input
                      type="radio"
                      name="visibility-mode"
                      value="prune"
                      checked
                    > Prune
                  </label>
                  <label class="btn btn-default">
                    <input type="radio" name="visibility-mode" value="hide">
                    Hide
                  </label>
                </div>

                <div class="form-group">
                  <label for="ndegslider">Node degree</label>
                  <output for="ndegslider" id="ndeglabel">0</output>
                  <input
                    type="range"
                    id="ndegslider"
                    value="0"
                    min="0"
                    max="200"
                  >
                </div>

                <div class="form-group">
                  <label for="wminslider">Minimum chemical contacts</label>
                  <output for="wminslider" id="wminlabel">1</output>
                  <input
                    type="range"
                    id="wminslider"
                    value="1"
                    min="1"
                    max="40"
                  >
                </div>

                <div class="form-group">
                  <label for="jminslider">Minimum electrical contacts</label>
                  <output for="jminslider" id="jminlabel">1</output>
                  <input
                    type="range"
                    id="jminslider"
                    value="1"
                    min="1"
                    max="25"
                  >
                </div>

                <div class="checkbox">
                  <label><input
                      type="checkbox"
                      id="show-synapses"
                      checked
                    >Chemical synapses</label>
                </div>
                <div class="checkbox">
                  <label><input
                      type="checkbox"
                      id="show-junctions"
                      checked
                    >Electrical junctions</label>
                </div>
                <div class="checkbox">
                  <label><input type="checkbox" id="show-arcs">Connections as
                    arcs</label>
                </div>
              </div>
            </details>
          </div>
        </div>
      </aside>

      <aside class="uiwidget uiwidget-right out" id="right-widget">
        <button
          type="button"
          class="uihandle uihandle-edge uihandle-right"
          id="right-handle"
          aria-controls="right-widget"
          aria-expanded="false"
          aria-label="Toggle info sidebar"
        >
          <span class="glyphicon glyphicon-chevron-left"></span>
        </button>

        <div class="uiwidget-body">
          <section class="formpanel formpanel-static">
            <div class="formpanel-heading">
              <span class="formpanel-title">Statistics</span>
            </div>
            <div class="panel-body">
              <ul class="list-group list-group-sm">
                <li class="list-group-item">
                  <span class="badge" id="stats-n">0</span>Neurons
                </li>
                <li class="list-group-item">
                  <span class="badge" id="stats-m">0</span>Muscles
                </li>
                <li class="list-group-item">
                  <span class="badge" id="stats-s">0</span>Chemical synapses
                </li>
                <li class="list-group-item">
                  <span class="badge" id="stats-ej">0</span>Electrical junctions
                </li>
                <li class="list-group-item">
                  <span class="badge" id="stats-nmj">0</span>NM junctions
                </li>
              </ul>
            </div>
          </section>

          <div class="uiwidget-scroll">
            <details class="formpanel" open>
              <summary><span id="node-heading">Node info</span></summary>
              <div class="panel-body" id="nodeinfo">Click to select...</div>
            </details>

            <details class="formpanel">
              <summary>Export</summary>
              <div class="panel-body">
                <p>Download the current fetched graph in a portable format.</p>
                <div class="form-group">
                  <label for="export-format">Format</label>
                  <select id="export-format" class="form-control input-sm">
                    <option value="json-list">JSON (node-link)</option>
                    <option value="json-graph">JSON (adjacency)</option>
                    <option value="graphml">GraphML</option>
                    <option value="gml">GML</option>
                    <option value="adj">Adjacency list</option>
                  </select>
                </div>
                <button
                  type="button"
                  id="export-button"
                  class="btn btn-default btn-sm btn-block"
                >
                  Export
                </button>
                <p class="export-divider">
                  Or download the current SVG view as an image.
                </p>
                <button
                  type="button"
                  id="download-png"
                  class="btn btn-default btn-sm btn-block"
                >
                  Download PNG
                </button>
              </div>
            </details>
          </div>
        </div>
      </aside>
    </main>

    <div id="footerwrapper">
      <div id="footer" class="noselect">
        <div class="legend-grid">
          <div>
            <strong>Neuron type</strong>
            <div class="legend-row">
              <span class="legend-dot sensory"></span>Sensory
            </div>
            <div class="legend-row">
              <span class="legend-dot inter"></span>Inter
            </div>
            <div class="legend-row">
              <span class="legend-dot motor"></span>Motor
            </div>
          </div>
          <div>
            <strong>Node size</strong>
            <div class="legend-row">Scaled by total degree</div>
            <div class="legend-row">Dashed border: selected</div>
            <div class="legend-row">Solid border: pinned</div>
          </div>
          <div>
            <strong>Edge type</strong>
            <div class="legend-row">
              <span class="legend-line synapse"></span>Synapse / NMJ
            </div>
            <div class="legend-row">
              <span class="legend-line ej"></span>Electrical junction
            </div>
          </div>
        </div>
      </div>
    </div>

    <script type="module" src="/src/main.js"></script>
  </body>
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