Team:Concordia

From 2013.igem.org

(Difference between revisions)
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     <li><a href="https://2013.igem.org/Team:Concordia/Attributions">Attributions</a></li></ul>
     <li><a href="https://2013.igem.org/Team:Concordia/Attributions">Attributions</a></li></ul>
</div>
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<div class="meny-arrow"></div><div class="contents">
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</div>
</div>
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  <div class="radial-menu-container clearfix">
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<div class="container">
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<a class='button ctrl' tabindex='1'></a>
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<ul class='tip ctrl'>
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    <div class="allContainer">
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<li class='slice'><a href='https://2013.igem.org/Team:Concordia/Project'>Project</a></li>
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      <div class="title">
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<li class='slice'><a href='https://2013.igem.org/Team:Concordia/Team'>Team</a></li>
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        <img src="img/logo.png" alt="logo"/>
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<li class='slice'><a href='https://2013.igem.org/Team:Concordia/HumanPractises'>HP</a></li>
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        <h1 class='text-right'>Numerical Analysis of Gene Regulatory Network Protein Synthesis and Decay</h1>
-
<li class='slice'><a href='https://2013.igem.org/Team:Concordia/Notebook'>Notebook</a></li>
+
      </div>
-
<li class='slice'><a href='https://2013.igem.org/Team:Concordia/Modeling'>Modeling</a></li>
+
      <h3 class="parameters-label section-expand">+ Parameters</h3 >
-
</ul>
+
      <div class="all-parameters" style='display:none;'>
 +
          <div class="parameter-section-row">
 +
          <!-- Gas -->
 +
          <div class="parameter-section">
 +
            <p class="section-collapse">&#45; Gas Protein 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="GasProteinHalfLifeInput" type="text" class="form-control" placeholder="20"> </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="GasProteinStrengthInput" type="text" class="form-control" placeholder="1"> </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="GasProteinSizeInput" type="text" class="form-control" placeholder="4"> </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="GasProteinThresholdInput" 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="GasProteinSensitivityInput" type="text" class="form-control" placeholder="3"> </input><span class="input-group-addon">units</span>
 +
                </div>
 +
              </div>
 +
              <li class="divider"></li>
 +
              <div class='parameter-control'>
 +
                <span class="parameter-control-label">Gas Prod factor:</span>
 +
                <div class="input-group">
 +
                <input id="GasProductionInput" type="text" class="form-control" placeholder="1"> </input><span class="input-group-addon">units</span>
 +
                </div>
 +
              </div>
 +
              <div class='parameter-control'>
 +
                <span class="parameter-control-label">Gas Diffusion rates:</span>
 +
                <div class="input-group">
 +
                <input id="GasDiffusionInput" type="text" class="form-control" placeholder="39.5"> </input><span class="input-group-addon">units</span>
 +
                </div>
 +
              </div>
 +
              <div class='parameter-control'>
 +
                <button id="bttnGraphGasRate" type="button" class="btn btn-default">Graph</button>
 +
              </div>
 +
              <div class='graph-container'>
 +
                <p class="section-collapse"> &#45; Rate of gas as a function of Gas Protein</p>
 +
                <div  id='gas-rate-graph' class='rate-graph'>
 +
                </div>
 +
                <p class="section-collapse"> &#45; Rate of Gas Protein as a function of Repressor</p>
 +
                <div  id='gas-protein-rate-graph' class='rate-graph'>
 +
                </div>
 +
              </div>
 +
            </div>
 +
          </div>
 +
          <!-- Repressor -->
 +
          <div class="parameter-section">
 +
            <p class="section-collapse">&#45; Repressor 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="RepressorHalfLifeInput" type="text" class="form-control" placeholder="20"> </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="RepressorStrengthInput" type="text" class="form-control" placeholder="4"> </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="RepressorSizeInput" type="text" class="form-control" placeholder="1"> </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="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">
 +
          <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>
 +
       
 +
       
 +
       
 +
        <!-- ******************* ROW 1 ******************* -->
 +
       
 +
       
 +
       
 +
        <div class="parameter-section-row">
 +
        <!-- Algorithmic -->
 +
          <div class="parameter-section">
 +
            <p class="section-expand">&#43; Algorithmic Parameters</p>
 +
            <div class='parameter-control-container' style='display: none;'>
 +
              <div class='parameter-control'>
 +
                <span class="parameter-control-label">Delta Time:</span>
 +
                <div class="input-group">
 +
                  <input id="DeltaTimeInput" type="text" class="form-control" placeholder="0.125"> </input><span class="input-group-addon">min</span>
 +
                </div>
 +
              </div>
 +
              <div class='parameter-control'>
 +
                <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>
 +
          </div>
 +
          <!-- Empty place holders TODO: Move beofre algo -->
 +
          <div class="parameter-section">
 +
            <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>
 +
            <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>
 +
          </div>
 +
          </div>
 +
          <div class="parameter-section">
 +
            <p class="section-collapse"></p>
 +
          </div>
 +
        </div>
 +
       
 +
       
 +
       
 +
        <!-- ******************* ROW 2 ******************* -->
 +
       
 +
       
 +
       
 +
        <div class="parameter-section-row" >
 +
          <button id="bttnRun" type="button" class="btn btn-primary">Run</button>
 +
        </div>
 +
      </div>
 +
      <li class='divider'></li>
 +
      <div class="dock">
 +
        <div class="graph-select">
 +
        <span class="graph-select-label">Gas Protein </span>
 +
        <div class="graph-group-dropdown-container">
 +
          <span class="graph-group-dropdown-label">group:</span>
 +
          <select id="gas-protein-group" class="graph-group-dropdown form-control" >
 +
           
 +
            <option selected="selected">1</option>
 +
            <option>2</option>
 +
            <option>3</option>
 +
            <option>4</option>
 +
            <option>5</option>
 +
          </select>
 +
          </div>
 +
        </div>
 +
        <div class="graph-select">
 +
          <span class="graph-select-label"> Gas</span>
 +
          <div class="graph-group-dropdown-container">
 +
          <span class="graph-group-dropdown-label">group:</span>
 +
          <select id="gas-group" class="graph-group-dropdown form-control">
 +
            <option>1</option>
 +
            <option selected="selected">2</option>
 +
            <option>3</option>
 +
            <option>4</option>
 +
            <option>5</option>
 +
          </select>
 +
          </div>
 +
        </div>
 +
        <div class="graph-select">
 +
          <span class="graph-select-label"> Gas Protein Repressor</span>
 +
          <div class="graph-group-dropdown-container">
 +
          <span class="graph-group-dropdown-label">group:</span>
 +
          <select id="repressor-group" class="graph-group-dropdown form-control" >
 +
            <option>1</option>
 +
            <option>2</option>
 +
            <option selected="selected">3</option>
 +
            <option>4</option>
 +
            <option>5</option>
 +
          </select>
 +
          </div>
 +
        </div>
 +
        <div class="graph-select">
 +
          <span class="graph-select-label">AHLR</span>
 +
          <div class="graph-group-dropdown-container">
 +
          <span class="graph-group-dropdown-label">group:</span>
 +
          <select id="ahlr-group" class="graph-group-dropdown form-control" >
 +
            <option>1</option>
 +
            <option>2</option>
 +
            <option>3</option>
 +
            <option selected="selected">4</option>
 +
            <option>5</option>
 +
          </select>
 +
          </div>
 +
        </div>
 +
        <div class="graph-select">
 +
          <span class="graph-select-label"> AHL Synthesis</span>
 +
          <div class="graph-group-dropdown-container">
 +
          <span class="graph-group-dropdown-label">group:</span>
 +
          <select id="ahl-group" class="form-control graph-group-dropdown" >
 +
            <option>1</option>
 +
            <option>2</option>
 +
            <option>3</option>
 +
            <option>4</option>
 +
            <option selected="selected">5</option>
 +
          </select>
 +
          </div>
 +
        </div>
 +
      </div>
 +
      <div class="graph-display">
 +
        <div class="graph-label section-collapse"> - Graph group 1</div>
 +
        <div id="graph-group1" class="graph"></div>
 +
        <div class="graph-label section-collapse"> - Graph group 2</div>
 +
        <div id="graph-group2" class="graph"></div>
 +
        <div class="graph-label section-collapse"> - Graph group 3</div>
 +
        <div id="graph-group3" class="graph"></div>
 +
        <div class="graph-label section-collapse"> - Graph group 4</div>
 +
        <div id="graph-group4" class="graph"></div>
 +
        <div class="graph-label section-collapse"> - Graph group 5</div>
 +
        <div id="graph-group5" class="graph"></div>
 +
       
 +
      </div>
 +
      <li class='divider'></li>
 +
    </div>
 +
 +
 +
<div class="description">
 +
      <h2>Governing equations</h2>
 +
      <h3>Gas production/dissipation</h3>
 +
      <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,
 +
        $$
 +
        {dQ_{rep}\over dt} = \left\{
 +
        \begin{array}{l l}
 +
          -{Q_{rep} \cdot ln(1/2) \over \tau_{\text{rep-halflife}} } + R_{prom\_str} \cdot R_{size\_fact} - R_{prom\_str} \cdot R_{size\_fact} \cdot e ^ { {- ( Q_{gas} - R_{thresh} ) / R_{thresh\_sensitivity} }} & \quad \text{if $Q_{gas} >= R_{thresh}$ }\\
 +
          -{Q_{rep} \cdot ln(1/2) \over \tau_{\text{rep-halflife}} }  & \quad \text{o.w. }
 +
        \end{array} \right.
 +
        $$
 +
</p>
 +
      <br><br>
 +
      <p>
 +
        &copy; COMPUT-E.COLI, Gabriel Belmonte<br/>
 +
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 +
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Revision as of 06:27, 27 September 2013

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Numerical Analysis of Gene Regulatory Network Protein Synthesis and Decay

+ Parameters

  • Gas Protein
    group:
    Gas
    group:
    Gas Protein Repressor
    group:
    AHLR
    group:
    AHL Synthesis
    group:
    - Graph group 1
    - Graph group 2
    - Graph group 3
    - Graph group 4
    - Graph group 5

  • Governing equations

    Gas production/dissipation

    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, $$ {dQ_{gas} \over dt} = P_{gas} \cdot Q_{gp} - D_{gas} $$


    Gas Protein Production/Decay

    The production of the gas protein is affected negatively by its size, and positively by the promoter strength.

    Given enough repressor, the production of the protein drops exponentially to zero.
    Furthermore, it degrades with a given half-life.
    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.
    For this reason, the half-life is present regardless of the amount of repressor.
    The second part is the production.

    On the second equation, if the repressor is at small quantities, then the production is uninhibited.
    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.
    The larger this factor, the slower the switch-off/switch-on.


    Repressor Production/Decay

    The repressor is promoted by the presence of gas. It will not be produced, if there is no gas.
    There has to be enough gas for the repressor to be generated. This is the repressor's threshold.
    The repressor itself has a half-life.
    Thus, $$ {dQ_{rep}\over dt} = \left\{ \begin{array}{l l} -{Q_{rep} \cdot ln(1/2) \over \tau_{\text{rep-halflife}} } + R_{prom\_str} \cdot R_{size\_fact} - R_{prom\_str} \cdot R_{size\_fact} \cdot e ^ { {- ( Q_{gas} - R_{thresh} ) / R_{thresh\_sensitivity} }} & \quad \text{if $Q_{gas} >= R_{thresh}$ }\\ -{Q_{rep} \cdot ln(1/2) \over \tau_{\text{rep-halflife}} } & \quad \text{o.w. } \end{array} \right. $$



    © COMPUT-E.COLI, Gabriel Belmonte
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