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  <meta name="Description" content="MicrobeTrace is an interactive web application that renders existing data from high-risk contact networks in an easy-to-use Graphical User Interface (GUI). The network visualization can be customized according to supplemental data sources and mathematical inferences like the most probable transmission pathways. MicrobeTrace is a highly responsive, visual sequence analytics tool which can reduce the gap between data production and analytics and help you to discover, understand, and display relationships (links) between patients (nodes). MicrobeTrace can be deployed on laptops to locations without any Internet access, thereby reducing both the startup cost and analysis time and effort.">
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      <li><span id="development-version" style="margin-left: 40px; color: #0037ff; font-weight: bolder; font-size: x-small;"> non production environment </span></li>

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          <input type="search" id="search" class="form-control form-control-sm" placeholder="Nodes">
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      <!-- #298 -->
      <button id="casesensitivebutton" type="button" class="btn btn-light btn-sm" data-toggle="button" aria-pressed="false" autocomplete="off" title="Match Case">
        <span>C</span>
      </button>     
      <button id="wholewordbutton" type="button" class="btn btn-light btn-sm" data-toggle="button" aria-pressed="false" autocomplete="off" title="Match Whole Word">
        <span>W</span>
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      <select id="search-field" class="form-control form-control-sm nodeValues">
        <option val="id">ID</option>
      </select>
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          <pre>The material embodied in this software is provided to you "As-is" and without
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the Centers for Disease Control and Prevention (CDC) or the United States (U.S.)
government be liable to you or anyone else for any direct, special, incidental,
indirect or consequential damages of any kind, or any damages whatsoever,
including without limitation, loss of profit, loss of use, savings or revenue,
or the claims of third parties, whether or not CDC or the U.S. Government has
been advised of the possibility of such loss, however caused and on any theory
of liability, arising out of or in connection with the possession, use or
performance of this software.</pre>
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          <span id="numberOfNodes"></span>
          (<span id="numberOfSelectedNodes"></span>)
        </td>
        <td>Nodes (Selected)</td>
      </tr>
      <tr>
        <td id="numberOfVisibleLinks" class="text-right"></td>
        <td>Links</td>
      </tr>
      <tr>
        <td id="numberOfDisjointComponents" class="text-right"></td>
        <td>Clusters</td>
      </tr>
      <tr>
        <td id="numberOfSingletonNodes" class="text-right"></td>
        <td>Singletons</td>
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    <a href="#" id="moveStats" class="dropdown-item">Drag/Arrow Keys</a>
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          <h5 class="modal-title">Global Settings</h5>
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            <span aria-hidden="true">&times;</span>
          </button>
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          <ul class="nav nav-tabs" role="tablist">
            <li class="nav-item active">
              <a class="nav-link active" id="filtering-tab" data-toggle="tab" href="#filtering-config" role="tab" aria-controls="home" aria-selected="true">Filtering</a>
            </li>
            <li class="nav-item">
              <a class="nav-link" id="style-tab" data-toggle="tab" href="#style-config" role="tab" aria-controls="home" aria-selected="true">Styling</a>
            </li>
            <li class="nav-item">
              <a class="nav-link" id="timeline-tab" data-toggle="tab" href="#timeline-config" role="tab" aria-controls="home" aria-selected="true">Timeline</a>
            </li>
          </ul>
          <div class="tab-content">
            <div class="tab-pane fade show active" id="filtering-config" role="tabpanel" aria-labelledby="filtering-tab">
              <div class="form-group row" title="By what algorithm would you like to prune links from the network?">
                <div class="col-4">Prune With</div>
                <div class="col-8">
                  <div class="btn-group btn-group-toggle btn-group-sm w-100" data-toggle="buttons">
                    <label class="btn btn-light active col" title="Show all links within threshold">
                      <input type="radio" name="NNOptions" id="link-show-all" autocomplete="off" checked> None
                    </label>
                    <label class="btn btn-light col" title="Prune links by Nearest Neighbor">
                      <input type="radio" name="NNOptions" id="link-show-nn" autocomplete="off"> Nearest Neighbor
                    </label>
                  </div>
                </div>
              </div>
              <div id="filtering-epsilon-row" class="form-group row" title="How much genetic distance represents non-equality for your ">
                <div class="col-4"><label for="filtering-epsilon">Filtering Epsilon</label></div>
                <div class="col-8">
                  <input type="range" class="custom-range" id="filtering-epsilon" min="-3" max="2" step=".01" value="-3">
                </div>
                <div class="col-8 offset-4">
                  <input type="number" id="filtering-epsilon-copy" class="form-control form-control-sm" disabled>
                </div>
              </div>
              <div class="form-group row" title="What's the minimum number of nodes a cluster must have in order to be visible?">
                <div class="col-4">
                  <label for="cluster-minimum-size">Minimum Cluster Size</label>
                </div>
                <div class="col-8">
                  <input type="number" class="form-control form-control-sm" id="cluster-minimum-size" min="1" value="1" step="1">
                </div>
              </div>
              <div id="filtering-wrapper">
                <div class="form-group row" title="By what variable would you like to prune links from the network?">
                  <div class="col-4"><label for="link-sort-variable">Filter Links on</label></div>
                  <div class="col-8">
                    <select id="link-sort-variable" class="form-control form-control-sm linkVariables">
                      <option value="distance" selected>Distance</option>
                    </select>
                  </div>
                </div>
                <div class="form-group row" title="What's the maximum genetic distance you're willing to call a link?">
                  <div class="col-4"><label for="link-threshold">Filtering Threshold</label></div>
                  <div class="col-8"><svg id="link-threshold-sparkline"></svg></div>
                  <div class="col-8 offset-4">
                    <input type="number" class="form-control form-control-sm" id="link-threshold" step="0.001">
                  </div>
                </div>
              </div>
              <div class="form-group row" title="Click to reveal all hidden elements of the network.">
                <div class="col-4"><label for="RevealAllTab">Reveal</label></div>
                <div class="col-8">
                  <button id="RevealAllTab" type="button" class="btn btn-light btn-sm w-100">Everything</button>
                </div>
              </div>
              <hr>
              <div class="form-group row" title="Display a table of overview statistics for the network">
                <div class="col-4">Statistics</div>
                <div class="col-8">
                  <div class="btn-group btn-group-toggle btn-group-sm w-100" data-toggle="buttons">
                    <label class="btn btn-light active col" title="Show a table of overview statistics for the network">
                      <input type="radio" name="network-statistics-visibility" id="network-statistics-show" autocomplete="off" checked>
                      Show
                    </label>
                    <label class="btn btn-light col" title="Do not show a table of overview statistics for the network">
                      <input type="radio" name="network-statistics-visibility" id="network-statistics-hide" autocomplete="off">
                      Hide
                    </label>
                  </div>
                </div>
              </div>
            </div>
            <div class="tab-pane fade" id="style-config" role="tabpanel" aria-labelledby="style-tab">
              <div class="form-group row" title="By what variable nodes be colored?">
                <div class="col-4"><label for="node-color-variable">Color Nodes By</label></div>
                <div class="col-8">
                  <select id="node-color-variable" class="form-control form-control-sm nodeVariables">
                    <option>None</option>
                  </select>
                </div>
              </div>
              <div id="node-color-table-row" class="form-group row" title="Should MicrobeTrace display the table of colors?">
                <div class="col-4">Node Color Table</div>
                <div class="col-8">
                  <div class="btn-group btn-group-toggle btn-group-sm w-100" data-toggle="buttons">
                    <label class="btn btn-light active col">
                      <input type="radio" name="nodeColorTableShowHide" id="node-color-table-show" autocomplete="off" checked>
                      Show
                    </label>
                    <label class="btn btn-light col">
                      <input type="radio" name="nodeColorTableShowHide" id="node-color-table-hide" autocomplete="off">
                      Hide
                    </label>
                  </div>
                </div>
              </div>
              <div id="node-color-value-row" class="form-group row" title="What color should the nodes be?">
                <div class="col-4"><label for="node-color">Nodes</label></div>
                <div class="col-8">
                  <input type="color" id="node-color" class="form-control form-control-sm" value="#1f77b4">
                </div>
              </div>
              <div class="form-group row" title="What color should the node border be?">
                <div class="col-4"><label for="node-color-border">Node Border</label></div>
                <div class="col-8">
                  <input type="color" id="node-color-border" class="form-control form-control-sm" value="#000000">
                </div>
              </div>
              <div class="form-group row" title="By what variable should links be colored?">
                <div class="col-4"><label for="link-color-variable">Color Links By</label></div>
                <div class="col-8">
                  <select id="link-color-variable" class="form-control form-control-sm linkVariables">
                    <option>None</option>
                  </select>
                </div>
              </div>
              <div id="link-color-table-row" class="form-group row" title="Should MicrobeTrace display the table of colors?">
                <div class="col-4">Link Color Table</div>
                <div class="col-8">
                  <div class="btn-group btn-group-toggle btn-group-sm w-100" data-toggle="buttons">
                    <label class="btn btn-light active col">
                      <input type="radio" name="linkColorTableShowHide" id="link-color-table-show" autocomplete="off" checked>
                      Show
                    </label>
                    <label class="btn btn-light col">
                      <input type="radio" name="linkColorTableShowHide" id="link-color-table-hide" autocomplete="off">
                      Hide
                    </label>
                  </div>
                </div>
              </div>
              <div id="link-color-value-row" class="form-group row" title="What color should the links be?">
                <div class="col-4"><label for="link-color">Links</label></div>
                <div class="col-8">
                  <input type="color" id="link-color" class="form-control form-control-sm" value="#a6cee3">
                </div>
              </div>
              <div class="form-group row" title="What color should denote selection?">
                <div class="col-4"><label for="selected-color">Selected</label></div>
                <div class="col-8">
                  <input type="color" id="selected-color" class="form-control form-control-sm" value="#ff8300">
                </div>
              </div>
              <div class="form-group row" title="What color should the background be?">
                <div class="col-4"><label for="background-color">Background</label></div>
                <div class="col-8">
                  <input type="color" id="background-color" class="form-control form-control-sm" value="#ffffff">
                </div>
              </div>
              <div class="form-group row" title="Load an existing MicrobeTrace style file">
                <div class="col-4">Apply Style</div>
                <div class="col-8">
                  <input type="file" id="apply-style" class="d-none">
                  <label class="custom-file-label" for="apply-style">Choose MicrobeTrace Style File</label>
                </div>
              </div>
            </div>
            <div class="tab-pane fade" id="timeline-config" role="tabpanel" aria-labelledby="timeline-tab">
              <div class="form-group row" title="By what variable timeline applied?">
                <div class="col-4"><label for="node-timeline-variable">Timeline By</label></div>
                <div class="col-8">
                  <select id="node-timeline-variable" class="form-control form-control-sm nodeVariables">
                    <option>None</option>
                  </select>
                </div>
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          <h3>MicrobeTrace <small>v<span id="version"></span></small></h3>
          <p>
            MicrobeTrace is an interactive web application that renders existing data from high-risk contact networks
            in an easy-to-use Graphical User Interface (GUI). The network visualization can be customized according to
            supplemental data sources and mathematical inferences like the most probable transmission pathways.
            MicrobeTrace is a highly responsive, visual sequence analytics tool which can reduce the gap between data
            production and analytics and help you to discover, understand, and display relationships (links) between
            patients (nodes). MicrobeTrace can be deployed on laptops to locations without any Internet access, thereby
            reducing both the startup cost and analysis time and effort.
          </p>
          <p class="ifOnline">
            <a href="https://github.com/CDCgov/MicrobeTrace/wiki" target="_blank" rel="noreferrer noopener">
              Click Here to Learn More
            </a>
          </p>
          <p>
            MicrobeTrace was built by the Molecular Epidemiology and Bionformatics Team at the CDC in Atlanta.
            <a href="https://cdcgov.github.io/MEBT" target="_blank" rel="noreferrer noopener" class="ifOnline">
              Click Here to See MEBT's Other Tools
            </a>
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            <a href="humans.txt">
              <img src="img/humanstxt-isolated-blank.gif" title="Click to see our humans.txt file" alt="humans.txt">
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