Team:Concordia/Modeling

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      <div class="title">
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        <h1 class='text-right'>Numerical Analysis of Gene Regulatory Network Protein Synthesis and Decay</h1>
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      </div>
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      <h3 class="parameters-label section-expand">+ Parameters</h3 >
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      <div class="all-parameters" style='display:none;'>
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          <div class="parameter-section-row">
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          <!-- Gas -->
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          <div class="parameter-section">
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            <p class="section-collapse">&#45; Gas Protein synthesis parameters</p>
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            <div class='parameter-control-container'>
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              <div class='parameter-control'>
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                <span class="parameter-control-label">Half-life:</span>
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                <div class="input-group">
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                  <input id="GasProteinHalfLifeInput" type="text" class="form-control" placeholder="20"> </input><span class="input-group-addon">units</span>
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                </div>
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              </div>
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              <div class='parameter-control'>
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                <span class="parameter-control-label">Promoter Strength:</span>
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                <div class="input-group">
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                <input id="GasProteinStrengthInput" type="text" class="form-control" placeholder="1"> </input><span class="input-group-addon">units</span>
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                </div>
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              </div>
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              <div class='parameter-control'>
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                <span class="parameter-control-label">Protein Size Factor:</span>
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                <div class="input-group">
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                <input id="GasProteinSizeInput" type="text" class="form-control" placeholder="4"> </input><span class="input-group-addon">units</span>
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                </div>
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              </div>
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              <div class='parameter-control'>
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                <span class="parameter-control-label">Turn-off threshold:</span>
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                <div class="input-group">
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                <input id="GasProteinThresholdInput" type="text" class="form-control" placeholder="25"> </input><span class="input-group-addon">units</span>
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                </div>
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              </div>
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              <div class='parameter-control'>
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                <span class="parameter-control-label">Turn-off sensitivity:</span>
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                <div class="input-group">
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                <input id="GasProteinSensitivityInput" type="text" class="form-control" placeholder="3"> </input><span class="input-group-addon">units</span>
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                </div>
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              </div>
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              <li class="divider"></li>
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              <div class='parameter-control'>
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                <span class="parameter-control-label">Gas Prod factor:</span>
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                <div class="input-group">
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                <input id="GasProductionInput" type="text" class="form-control" placeholder="1"> </input><span class="input-group-addon">units</span>
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                </div>
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              </div>
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              <div class='parameter-control'>
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                <span class="parameter-control-label">Gas Diffusion rates:</span>
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                <div class="input-group">
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                <input id="GasDiffusionInput" type="text" class="form-control" placeholder="39.5"> </input><span class="input-group-addon">units</span>
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                </div>
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              </div>
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              <div class='parameter-control'>
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                <button id="bttnGraphGasRate" type="button" class="btn btn-default">Graph</button>
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              </div>
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              <div class='graph-container'>
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                <p class="section-collapse"> &#45; Rate of gas as a function of Gas Protein</p>
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                <div  id='gas-rate-graph' class='rate-graph'>
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                </div>
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                <p class="section-collapse"> &#45; Rate of Gas Protein as a function of Repressor</p>
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                <div  id='gas-protein-rate-graph' class='rate-graph'>
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                </div>
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              </div>
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            </div>
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          </div>
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          <!-- Repressor -->
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          <div class="parameter-section">
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            <p class="section-collapse">&#45; Repressor synthesis parameters</p>
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            <div class='parameter-control-container'>
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              <div class='parameter-control'>
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                <span class="parameter-control-label">Half-life:</span>
+
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                <div class="input-group">
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                  <input id="RepressorHalfLifeInput" type="text" class="form-control" placeholder="20"> </input><span class="input-group-addon">units</span>
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                </div>
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              </div>
+
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              <div class='parameter-control'>
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                <span class="parameter-control-label">Promoter Strength:</span>
+
-
                <div class="input-group">
+
-
                <input id="RepressorStrengthInput" type="text" class="form-control" placeholder="4"> </input><span class="input-group-addon">units</span>
+
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                </div>
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              </div>
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              <div class='parameter-control'>
+
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                <span class="parameter-control-label">Protein Size Factor:</span>
+
-
                <div class="input-group">
+
-
                <input id="RepressorSizeInput" type="text" class="form-control" placeholder="1"> </input><span class="input-group-addon">units</span>
+
-
                </div>
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              </div>
+
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              <div class='parameter-control'>
+
-
                <span class="parameter-control-label">Turn-off threshold:</span>
+
-
                <div class="input-group">
+
-
                <input id="RepressorThresholdInput" type="text" class="form-control" placeholder="25"> </input><span class="input-group-addon">units</span>
+
-
                </div>
+
-
              </div>
+
-
              <div class='parameter-control'>
+
-
                <span class="parameter-control-label">Turn-off sensitivity:</span>
+
-
                <div class="input-group">
+
-
                <input id="RepressorSensitivityInput" type="text" class="form-control" placeholder="3"> </input><span class="input-group-addon">units</span>
+
-
                </div>
+
-
              </div>
+
-
              <div class='parameter-control'>
+
-
                <button id="bttnGraphRepRate" type="button" class="btn btn-default">Graph</button>
+
-
              </div>
+
-
              <div class='graph-container'>
+
-
                <p class="section-collapse"> &#45; Rate of Repressor as a function of Gas</p>
+
-
                <div  id='rep-rate-graph' class='rate-graph'>
+
-
                </div>
+
-
              </div>
+
-
            </div>
+
-
          </div>
+
-
          <!-- AHLR -->
+
-
          <div class="parameter-section">
+
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          <p class="section-collapse"> &#45; AHLR synthesis parameters</p>
+
-
          <div class='parameter-control-container'>
+
-
            <div class='parameter-control'>
+
-
              <span class="parameter-control-label">Half-life:</span>
+
-
              <div class="input-group">
+
-
                <input  id="AhlrHalfLifeInput" type="text" class="form-control" placeholder="default"> </input><span class="input-group-addon">units</span>
+
-
              </div>
+
-
            </div>
+
-
            <div class='parameter-control'>
+
-
              <span class="parameter-control-label">Promoter Strength:</span>
+
-
              <div class="input-group">
+
-
              <input  id="AhlrStrengthInput" type="text" class="form-control" placeholder="default"> </input><span class="input-group-addon">units</span>
+
-
              </div>
+
-
            </div>
+
-
            <div class='parameter-control'>
+
-
              <span class="parameter-control-label">Protein Size Factor:</span>
+
-
              <div class="input-group">
+
-
              <input id="AhlrSizeInput" type="text" class="form-control" placeholder="default"> </input><span class="input-group-addon">units</span>
+
-
              </div>
+
-
            </div>
+
-
            <div class='parameter-control'>
+
-
              <span class="parameter-control-label">Turn-off threshold:</span>
+
-
              <div class="input-group">
+
-
              <input id="AhlrThresholdInput" type="text" class="form-control" placeholder="default"> </input><span class="input-group-addon">units</span>
+
-
              </div>
+
-
            </div>
+
-
            <div class='parameter-control'>
+
-
              <span class="parameter-control-label">Turn-off sensitivity:</span>
+
-
              <div class="input-group">
+
-
              <input id="AhlrSensitivityInput" type="text" class="form-control" placeholder="default"> </input><span class="input-group-addon">units</span>
+
-
              </div>
+
-
            </div>
+
-
          </div>
+
-
        </div>
+
-
        </div>
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-
       
+
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+
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-
        <!-- ******************* ROW 1 ******************* -->
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        <div class="parameter-section-row">
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        <!-- Algorithmic -->
+
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          <div class="parameter-section">
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-
            <p class="section-expand">&#43; Algorithmic Parameters</p>
+
-
            <div class='parameter-control-container' style='display: none;'>
+
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              <div class='parameter-control'>
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                <span class="parameter-control-label">Delta Time:</span>
+
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                <div class="input-group">
+
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                  <input id="DeltaTimeInput" type="text" class="form-control" placeholder="0.125"> </input><span class="input-group-addon">min</span>
+
-
                </div>
+
-
              </div>
+
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              <div class='parameter-control'>
+
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                <span class="parameter-control-label">Data-to-Graph Ratio:</span>
+
-
                <div class="input-group">
+
-
                <input id='DataToGraphPointRatioInput' type="text" class="form-control" placeholder="3"> </input><span class="input-group-addon">N/A</span>
+
-
                </div>
+
-
              </div>
+
-
              <div class='parameter-control'>
+
-
                <span class="parameter-control-label">Data size:</span>
+
-
                <div class="input-group">
+
-
                <input id="DataSizeInput" type="text" class="form-control" placeholder="3200"> </input><span class="input-group-addon">N/A</span>
+
-
                </div>
+
-
              </div>
+
-
            </div>
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          </div>
+
-
          <!-- Empty place holders TODO: Move beofre algo -->
+
-
          <div class="parameter-section">
+
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            <p class="section-collapse"> - AHL Parameters</p>
+
-
            <div class='parameter-control-container'>
+
-
            <div class='parameter-control'>
+
-
              <span class="parameter-control-label">Half-life:</span>
+
-
              <div class="input-group">
+
-
                <input  id="AhlHalfLifeInput" type="text" class="form-control" placeholder="default"> </input><span class="input-group-addon">units</span>
+
-
              </div>
+
-
            </div>
+
-
            <div class='parameter-control'>
+
-
              <span class="parameter-control-label">Promoter Strength:</span>
+
-
              <div class="input-group">
+
-
              <input  id="AhlStrengthInput" type="text" class="form-control" placeholder="default"> </input><span class="input-group-addon">units</span>
+
-
              </div>
+
-
            </div>
+
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            <div class='parameter-control'>
+
-
              <span class="parameter-control-label">Protein Size Factor:</span>
+
-
              <div class="input-group">
+
-
              <input id="AhlSizeInput" type="text" class="form-control" placeholder="default"> </input><span class="input-group-addon">units</span>
+
-
              </div>
+
-
            </div>
+
-
            <div class='parameter-control'>
+
-
              <span class="parameter-control-label">Turn-off threshold:</span>
+
-
              <div class="input-group">
+
-
              <input id="AhlThresholdInput" type="text" class="form-control" placeholder="default"> </input><span class="input-group-addon">units</span>
+
-
              </div>
+
-
            </div>
+
-
            <div class='parameter-control'>
+
-
              <span class="parameter-control-label">Turn-off sensitivity:</span>
+
-
              <div class="input-group">
+
-
              <input id="AhlSensitivityInput" type="text" class="form-control" placeholder="default"> </input><span class="input-group-addon">units</span>
+
-
              </div>
+
-
            </div>
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-
          </div>
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          </div>
+
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          <div class="parameter-section">
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            <p class="section-collapse"></p>
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          </div>
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        </div>
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        <!-- ******************* ROW 2 ******************* -->
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        <div class="parameter-section-row" >
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          <button id="bttnRun" type="button" class="btn btn-primary">Run</button>
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        </div>
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      </div>
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      <li class='divider'></li>
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      <div class="dock">
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        <div class="graph-select">
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        <span class="graph-select-label">Gas Protein </span>
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        <div class="graph-group-dropdown-container">
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          <span class="graph-group-dropdown-label">group:</span>
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          <select id="gas-protein-group" class="graph-group-dropdown form-control" >
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            <option selected="selected">1</option>
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            <option>2</option>
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            <option>3</option>
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            <option>4</option>
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            <option>5</option>
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          </select>
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          </div>
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        </div>
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        <div class="graph-select">
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          <span class="graph-select-label"> Gas</span>
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          <div class="graph-group-dropdown-container">
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          <span class="graph-group-dropdown-label">group:</span>
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          <select id="gas-group" class="graph-group-dropdown form-control">
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            <option>1</option>
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            <option selected="selected">2</option>
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            <option>3</option>
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            <option>4</option>
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            <option>5</option>
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          </select>
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          </div>
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        </div>
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        <div class="graph-select">
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          <span class="graph-select-label"> Gas Protein Repressor</span>
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          <div class="graph-group-dropdown-container">
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          <span class="graph-group-dropdown-label">group:</span>
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          <select id="repressor-group" class="graph-group-dropdown form-control" >
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            <option>1</option>
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            <option>2</option>
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            <option selected="selected">3</option>
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            <option>4</option>
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            <option>5</option>
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          </select>
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          </div>
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        </div>
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        <div class="graph-select">
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          <span class="graph-select-label">AHLR</span>
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          <div class="graph-group-dropdown-container">
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          <span class="graph-group-dropdown-label">group:</span>
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          <select id="ahlr-group" class="graph-group-dropdown form-control" >
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            <option>1</option>
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            <option>2</option>
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            <option>3</option>
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            <option selected="selected">4</option>
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            <option>5</option>
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          </select>
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          </div>
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        </div>
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        <div class="graph-select">
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          <span class="graph-select-label"> AHL Synthesis</span>
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          <div class="graph-group-dropdown-container">
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          <span class="graph-group-dropdown-label">group:</span>
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          <select id="ahl-group" class="form-control graph-group-dropdown" >
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            <option>1</option>
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            <option>2</option>
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            <option>3</option>
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            <option>4</option>
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            <option selected="selected">5</option>
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          </select>
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          </div>
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        </div>
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      </div>
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      <div class="graph-display">
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        <div class="graph-label section-collapse"> - Graph group 1</div>
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        <div id="graph-group1" class="graph"></div>
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        <div class="graph-label section-collapse"> - Graph group 2</div>
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        <div id="graph-group2" class="graph"></div>
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        <div class="graph-label section-collapse"> - Graph group 3</div>
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        <div id="graph-group3" class="graph"></div>
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        <div class="graph-label section-collapse"> - Graph group 4</div>
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        <div id="graph-group4" class="graph"></div>
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        <div class="graph-label section-collapse"> - Graph group 5</div>
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        <div id="graph-group5" class="graph"></div>
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      </div>
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      <li class='divider'></li>
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    </div>
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<div class="description">
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      <h2>Governing equations</h2>
+
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      <h3>Gas production/dissipation</h3>
+
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      <p>
+
-
The rate of production of gas is proportional to the amount of gas protein in the system, and some gas
+
-
        dissipates at a constant rate. Thus,       
+
-
        $$ {dQ_{gas} \over dt}  = P_{gas} \cdot Q_{gp} - D_{gas}  $$
+
-
</p><br>
+
-
      <h3>Gas Protein Production/Decay</h3>
+
-
<p>
+
-
        The production of the gas protein is affected negatively by its size,
+
-
        and positively by the promoter strength. <br><br>
+
-
        Given enough repressor, the production of the protein drops exponentially to zero.<br>
+
-
        Furthermore, it degrades with a given half-life. <br>
+
-
        Thus,
+
-
        $$
+
-
        {dQ_{gp}\over dt} = \left\{
+
-
        \begin{array}{l l}
+
-
          -{Q_{gp} \cdot ln(1/2) \over \tau_{\text{gp-halflife}} } + P_{prom\_str} \cdot P_{size\_fact} \cdot e ^ { {- ( Q_{rep} - P_{thresh} ) / P_{thresh\_sensitivity} }} & \quad \text{if $Q_{rep} >= P_{thresh}$ }\\
+
-
          -{Q_{gp} \cdot ln(1/2) \over \tau_{\text{gp-halflife}} } + P_{prom\_str} \cdot P_{size\_fact}  & \quad \text{o.w. }
+
-
        \end{array} \right.
+
-
        $$
+
-
        Alright. The first half of this stuff is the half-life. Tau itself is the half-life.<br>
+
-
        For this reason, the half-life is present regardless of the amount of repressor.<br>
+
-
        The second part is the production. <br><br>
+
-
        On the second equation, if the repressor is at small quantities, then the production is uninhibited. <br>
+
-
        On the first equation, if there is enough repressor, the production quickly drops to zero, at an exponential rate.
+
-
        How sensitive, or quick this "switch-off" occurs is controlled by the threshold sensitivity.<br>
+
-
        The larger this factor, the slower the switch-off/switch-on.
+
-
</p><br>
+
-
      <h3>Repressor Production/Decay</h3>
+
-
<p>
+
-
The repressor is promoted by the presence of gas. It will not be produced, if there is no gas.<br>
+
-
        There has to be enough gas for the repressor to be generated. This is the repressor's threshold.<br>
+
-
        The repressor itself has a half-life.<br>
+
-
        Thus,
+
-
        $$
+
-
        {dQ_{rep}\over dt} = \left\{
+
-
        \begin{array}{l l}
+
-
          -{Q_{rep} \cdot ln(1/2) \over \tau_{\text{rep-halflife}} } + R_{prom\_str} \cdot R_{size\_fact} - R_{prom\_str} \cdot R_{size\_fact} \cdot e ^ { {- ( Q_{gas} - R_{thresh} ) / R_{thresh\_sensitivity} }} & \quad \text{if $Q_{gas} >= R_{thresh}$ }\\
+
-
          -{Q_{rep} \cdot ln(1/2) \over \tau_{\text{rep-halflife}} }  & \quad \text{o.w. }
+
-
        \end{array} \right.
+
-
        $$
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-
</p>
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-
      <br><br>
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      <p>
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-
        &copy; COMPUT-E.COLI, Gabriel Belmonte<br/>
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        Powered by:<br/>
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        &nbsp;&nbsp;<a href="https://developers.google.com/chart/">Google Visualization</a> for graphing<br/>
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        &nbsp;&nbsp;<a href="http://www.mathjax.org/">MathJax</a> for LaTeX math equation rendering.<br/>
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      </p>
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</div>
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</div>
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Revision as of 15:08, 27 September 2013

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