Team:Slovenia/ModelingInteractiveSimulations

From 2012.igem.org

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<div id="banner">
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<a style="position:absolute; top:0px; left:490px;" href="https://2012.igem.org/Main_Page"><b>iGEM 2012</b></a>
 
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</div>
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<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchDesignedTALregulators'><span>Designed TAL regulators</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchDesignedTALregulators'><span>Designed TAL regulators</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchMutualRepressorSwitch'><span>Mutual repressor switch</span></a></li>  
<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchMutualRepressorSwitch'><span>Mutual repressor switch</span></a></li>  
-
<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchPositiveFeedbackLoopSwitch'><span>Positive feedback loop switch</span></a></li>  
+
<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchPositiveFeedbackLoopSwitch'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/TheSwitchPositiveFeedbackLoopSwitch';" class="newtable"><tr class="newtable"><td class="newtable"><span>Positive feedback loop switch</span></td><td class="newtable"><img style="margin-right:-15px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
 +
    <li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchControls'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/TheSwitchControls';" class="newtable"><tr class="newtable"><td class="newtable"><span>Controls</span></td><td class="newtable"><img style="margin-right:-81px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>  
  </ul>
  </ul>
</li>
</li>
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<li><a href='https://2012.igem.org/Team:Slovenia/SafetyMechanismsEscapeTag'><span>Escape tag</span></a></li>  
<li><a href='https://2012.igem.org/Team:Slovenia/SafetyMechanismsEscapeTag'><span>Escape tag</span></a></li>  
<li><a href='https://2012.igem.org/Team:Slovenia/SafetyMechanismsTermination'><span>Termination</span></a></li>  
<li><a href='https://2012.igem.org/Team:Slovenia/SafetyMechanismsTermination'><span>Termination</span></a></li>  
-
<li><a href='https://2012.igem.org/Team:Slovenia/SafetyMechanismsMicrocapsuleDegradation'><span>Microcapsule degradation</span></a></li>  
+
    <li><a href="https://2012.igem.org/Team:Slovenia/SafetyMechanismsMicrocapsuleDegradation"><table  onclick="window.location = 'https://2012.igem.org/Team:Slovenia/SafetyMechanismsMicrocapsuleDegradation';" class="newtable"><tr class="newtable"><td class="newtable"><span>Microcapsule degradation</span></td><td class="newtable"><img style="margin-right:-15px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>  
  </ul>
  </ul>
</li>
</li>
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<li><a href='https://2012.igem.org/Team:Slovenia/ImplementationHepatitisC'><span>Hepatitis C</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/ImplementationHepatitisC'><span>Hepatitis C</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/ImplementationIschaemicHeartDisease'><span>Ischaemic heart disease</span></a></li>  
<li><a href='https://2012.igem.org/Team:Slovenia/ImplementationIschaemicHeartDisease'><span>Ischaemic heart disease</span></a></li>  
 +
    <li><a href='https://2012.igem.org/Team:Slovenia/ImplementationImpact'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/ImplementationImpact';" class="newtable"><tr class="newtable"><td class="newtable"><span>Impact</span></td><td class="newtable"><img style="margin-right:-86px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
 
 
  </ul>
  </ul>
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  <ul>
  <ul>
<li><a href='https://2012.igem.org/Team:Slovenia/Modeling'><span>Overview</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/Modeling'><span>Overview</span></a></li>
-
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingPK'><span>Pharmacokinetics</span></a></li>
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    <li><a href='https://2012.igem.org/Team:Slovenia/ModelingPK'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/ModelingPK';" class="newtable"><tr class="newtable"><td class="newtable"><span>Pharmacokinetics</span></td><td class="newtable"><img style="margin-right:-15px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingMethods'><span>Modeling methods</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingMethods'><span>Modeling methods</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingMutualRepressorSwitch'><span>Mutual repressor switch</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingMutualRepressorSwitch'><span>Mutual repressor switch</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingPositiveFeedbackLoopSwitch'><span>Positive feedback loop switch</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingPositiveFeedbackLoopSwitch'><span>Positive feedback loop switch</span></a></li>
-
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingQuantitativeModel'><span>Quantitative and stability model</span></a></li>  
+
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingQuantitativeModel'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/ModelingQuantitativeModel';" class="newtable"><tr class="newtable"><td class="newtable"><span>Experimental model</span></td><td class="newtable"><img style="margin-right:-15px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>  
-
<li><a href='https://2012.igem.org/Team:Slovenia/ModelingInteractiveSimulations'><span>Interactive simulations</span></a></li>
+
    <li><a href='https://2012.igem.org/Team:Slovenia/ModelingInteractiveSimulations'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/ModelingInteractiveSimulations';" class="newtable"><tr class="newtable"><td class="newtable"><span>Interactive simulations</span></td><td class="newtable"><img style="margin-right:-15px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
  </ul>
  </ul>
</li>
</li>
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  <ul>
  <ul>
<li><a href='https://2012.igem.org/Team:Slovenia/Notebook'><span>Experimental methods</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/Notebook'><span>Experimental methods</span></a></li>
-
<li><a href='https://2012.igem.org/Team:Slovenia/NotebookLablog'><span>Lablog</span></a></li>
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    <li><a href='https://2012.igem.org/Team:Slovenia/NotebookLablog'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/NotebookLablog';" class="newtable"><tr class="newtable"><td class="newtable"><span>Lablog</span></td><td class="newtable"><img style="margin-right:-90px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/NotebookLabSafety'><span>Lab safety</span></a></li>  
<li><a href='https://2012.igem.org/Team:Slovenia/NotebookLabSafety'><span>Lab safety</span></a></li>  
  </ul>
  </ul>
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<li><a href='https://2012.igem.org/Team:Slovenia/Team'><span>Team members</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/Team'><span>Team members</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/TeamAttributions'><span>Attributions</span></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/TeamAttributions'><span>Attributions</span></a></li>
 +
<li><a href='https://2012.igem.org/Team:Slovenia/TeamCollaborations'><table  onclick="window.location = 'https://2012.igem.org/Team:Slovenia/TeamCollaborations';" class="newtable"><tr class="newtable"><td class="newtable"><span>Collaborations</span></td><td class="newtable"><img style="margin-right:-20px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
<li><a href='https://2012.igem.org/Team:Slovenia/TeamGallery'><span>Gallery</span></a></li>  
<li><a href='https://2012.igem.org/Team:Slovenia/TeamGallery'><span>Gallery</span></a></li>  
<li><a href='https://2012.igem.org/Team:Slovenia/TeamSponsors'><span>Sponsors</span></a></li>  
<li><a href='https://2012.igem.org/Team:Slovenia/TeamSponsors'><span>Sponsors</span></a></li>  
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    <br/>
 +
    <h1>Experimental model interactive simulations </h1>
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    <br/>
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    <br/>
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-
    <h1>Quantitative model interactive simulations </h1>
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</a>
      
      
     <p>
     <p>
-
Based on experimental data, we constructed what we refer to as a quantitative model. Please see <a href="https://2012.igem.org/Team:Slovenia/ModelingQuantitativeModel">Quantitative and stability model</a> for details.</p>
+
    Based on experimental data, we constructed an experimental model. Please see <a href="https://2012.igem.org/Team:Slovenia/ModelingQuantitativeModel">Experimental model</a> for details of derivation. For old models (developed before European Regional Jamboree), <a href="https://2012.igem.org/Team:Slovenia/ModelingInteractiveSimulationsOld"> click here.</a></p>  
      
      
-
    <p>
 
-
      <ul style="margin-left:15px;">
 
-
        <li><a href="#model1">Mutual repressor switch simulation</a><br/></li>
 
-
        <li><a href="#model2">The positive feedback loop switch simulation</a><br/></li>
 
-
</ul>
 
-
</p>
 
-
<br />
 
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<br />
 
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    <h2><a name="model1"></a>Mutual repressor switch</h2>
 
      
      
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     <form name="form1" action="http://igem2012.fri.uni-lj.si:443/cellulator/bistable" target="_blank" method="GET">
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       <input type="hidden" name="check_submit" value="1"/>  
       <input type="hidden" name="check_submit" value="1"/>  
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      <b>INPUT VECTORS DOSAGE</b> <br/>
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 +
 +
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      <table class="invisibile" style="border-radius: 30px;  background:cyan;  padding:10px 10px 10px 10px;">
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      <tr class="invisibile">
        
        
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      .</td></tr>
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       <b>INPUT VECTORS DOSAGE</b> <br/>
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       <hr/>
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        <tr class="normal"><td class="normal">Construct</td><td class="normal">Dosage</td></tr>
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        </thead>
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        <tbody class="normal">
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      <tr class="normal"><td class="normal"><strong>[A]_pCMV_TAL-B:KRAB_BFP</strong> </td><td class="normal"> <input type="text" name="plasmid1" size="5" value="190" onKeyPress="return numbersonly(this, event)" maxlength="4"/> ng</td></tr>
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-
      <tr class="normal"><td class="normal"><strong>[B]_pCMV_TAL-A:KRAB_mCitrine</strong> </td><td class="normal"> <input type="text" name="plasmid2" size="5" value="180" onKeyPress="return numbersonly(this, event)" maxlength="4"/> ng</td></tr>
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-
      <tr class="normal"><td class="normal"><strong>pCMV_[PIR]_TAL-B:KRAB</strong> </td><td class="normal"> <input type="text" name="plasmid3" size="5" value="190" onKeyPress="return numbersonly(this, event)" maxlength="4"/> ng</td></tr>
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-
      <tr class="normal"><td class="normal"><strong>pCMV_[ETR]_TAL-A:KRAB</strong> </td><td class="normal"> <input type="text" name="plasmid4" size="5" value="180" onKeyPress="return numbersonly(this, event)" maxlength="4"/> ng</td></tr>
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-
      <tr class="normal"><td class="normal"><strong>pCMV_PIP:KRAB</strong> </td><td class="normal"> <input type="text" name="plasmid5" size="5" value="180" onKeyPress="return numbersonly(this, event)" maxlength="4"/> ng</td></tr>
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      <tr class="normal"><td class="normal"><strong>pCMV_E:KRAB </strong> </td><td class="normal"> <input type="text" name="plasmid6" size="5" value="180" onKeyPress="return numbersonly(this, event)" maxlength="4"/> ng</td></tr>
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      </tbody>
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      </table>
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      <font color="blue">(Enter dosages for corresponding plasmids.)</font><br /><br />
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       </p>
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 +
      <table style="border-radius: 30px;  background:cyan;  padding:10px 10px 10px 10px;" width="95%">
 +
      <th><tr><td  style="background: #0099FF;"><b><font color="white">The Switch</font></b></td><td></td></tr></th>
 +
      <th>
 +
        <tr><td>Construct</td><td>Dosage</td></tr>
 +
        </th>
 +
      <tr><td><img align="left" src="https://static.igem.org/mediawiki/2012/0/09/Svn12_qm_interactive_p0.png" width="300px"/></td><td> <input type="text" name="plasmid0" size="3" value="1" onKeyPress="return numbersonly2(this, event)" maxlength="3"/> ng</td></tr>
 +
      <tr><td><img align="left" src="https://static.igem.org/mediawiki/2012/2/28/Svn12_qm_interactive_p1.png" width="200px"/><td> <input type="text" name="plasmid1" size="3" value="1" onKeyPress="return numbersonly2(this, event)" maxlength="3"/> ng</td></tr>
 +
      <tr><td><img align="left" src="https://static.igem.org/mediawiki/2012/f/f0/Svn12_qm_interactive_p2.png" width="300px"/><td> <input type="text" name="plasmid2" size="3" value="1" onKeyPress="return numbersonly2(this, event)" maxlength="3"/> ng</td></tr>
 +
      <tr><td><img align="left" src="https://static.igem.org/mediawiki/2012/7/70/Svn12_qm_interactive_p3.png" width="200px"/><td> <input type="text" name="plasmid3" size="3" value="1" onKeyPress="return numbersonly2(this, event)" maxlength="3"/> ng</td>
 +
      <tr><td></td><td></td></tr>
        
        
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       <div style="clear:both;"></div>
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       <th><tr><td  style="background: #0099FF;"><b><font color="white">Inducible system</font></b></td><td></td></tr></th>
-
        
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      <th>
 +
        <tr><td>Construct</td><td>Dosage</td></tr>
 +
        </th>
 +
       <tr><td><img align="left" src="https://static.igem.org/mediawiki/2012/c/cf/Svn12_qm_interactive_p4.png" width="200px"/><td> <input type="text" name="plasmid4" size="3" value="5" onKeyPress="return numbersonly2(this, event)" maxlength="3"/> ng</td></tr>
 +
      <tr><td><img align="left" src="https://static.igem.org/mediawiki/2012/f/f7/Svn12_qm_interactive_p5.png" width="200px"/><td> <input type="text" name="plasmid5" size="3" value="5" onKeyPress="return numbersonly2(this, event)" maxlength="3"/> ng</td></tr>
 +
      <tr><td><img align="left" src="https://static.igem.org/mediawiki/2012/9/96/Svn12_qm_interactive_p6.png" width="200px"/><td> <input type="text" name="plasmid6" size="3" value="5" onKeyPress="return numbersonly2(this, event)" maxlength="3"/> ng</td></tr>
 +
      <tr><td><img align="left" src="https://static.igem.org/mediawiki/2012/9/9f/Svn12_qm_interactive_p7.png" width="200px"/><td> <input type="text" name="plasmid7" size="3" value="5" onKeyPress="return numbersonly2(this, event)" maxlength="3"/> ng</td></tr>
 +
      <tr><td></td><td></td></tr>
 +
      <th><tr><td  style="background: #0099FF;"><b><font color="white">Pristinamycin/Erithromycin ind. proteins</font></b></td><td></td></tr></th>
 +
      <th>
 +
        <tr><td>Construct</td><td>Dosage</td></tr>
 +
        </th>
 +
      <tr><td><img align="left" src="https://static.igem.org/mediawiki/2012/6/6a/Svn12_qm_interactive_p8.png" width="200px"/><td> <input type="text" name="plasmid8" size="3" value="30" onKeyPress="return numbersonly2(this, event)" maxlength="3"/> ng</td></tr>
 +
      <tr><td><img align="left" src="https://static.igem.org/mediawiki/2012/b/b1/Svn12_qm_interactive_p9.png" width="200px"/><td> <input type="text" name="plasmid9" size="3" value="30" onKeyPress="return numbersonly2(this, event)" maxlength="3"/> ng</td></tr>
 +
      </table>
 +
      <font color="blue">(Enter dosages for corresponding plasmids. <font color="black">To comply with the jetPEI® protocol, the sum of masses shall not exceed 1000 ng. </font>)</font><br /><br />
        
        
 +
      </td>
 +
      <td class="invisibile" valign="top">
 +
           
 +
      <b>INDUCERS</b> <br/>
       <hr/>
       <hr/>
-
      <b>TRANSCRIPTION FACTORS</b>
 
-
      <br />
 
-
      <input type="checkbox" name="req" value="1" /> Equal transcription factors
 
-
      <br/>
 
-
      <font color="blue">(Transcription factors will alter transcription with equal rates)</font><br /> <br />
 
        
        
-
      <hr/>
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       <table style="border-radius: 30px;  background:cyan;  padding:10px 10px 10px 10px;">
-
      <b>INDUCERS</b> <br/>
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        <th><tr><td style="background: #0099FF;"><b><font color="white">Pristinamycin</font></b></td><td></td></tr></th>
-
     
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       <table>
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      <th><tr><td><i>Pristinamycin</i></td><td></td></tr></th>
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       <tr>
       <tr>
         <td>Input times [min]</td>
         <td>Input times [min]</td>
-
         <td><input type="text" name="pc_start1" size="5" value="2000" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
+
         <td><input type="text" name="pc_start1" size="5" value="200" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
-
         <td><input type="text" name="pc_start2" size="5" value="10000" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
+
         <td><input type="text" name="pc_start2" size="5" value="5000" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
         <td><input type="text" name="pc_start3" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
         <td><input type="text" name="pc_start3" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
         <td><input type="text" name="pc_start4" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
         <td><input type="text" name="pc_start4" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
Line 481: Line 493:
       <tr>
       <tr>
         <td>Durations [min]</td>
         <td>Durations [min]</td>
-
         <td><input type="text" name="pc_duration1" size="5" value="1000" onKeyPress="return numbersonly(this, event)" maxlength="6"><br/></td>
+
         <td><input type="text" name="pc_duration1" size="5" value="200" onKeyPress="return numbersonly(this, event)" maxlength="6"><br/></td>
-
         <td><input type="text" name="pc_duration2" size="5" value="1000" onKeyPress="return numbersonly(this, event)" maxlength="6"><br/></td>
+
         <td><input type="text" name="pc_duration2" size="5" value="300" onKeyPress="return numbersonly(this, event)" maxlength="6"><br/></td>
         <td><input type="text" name="pc_duration3" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"><br/></td>
         <td><input type="text" name="pc_duration3" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"><br/></td>
         <td><input type="text" name="pc_duration4" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"><br/></td>
         <td><input type="text" name="pc_duration4" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"><br/></td>
Line 491: Line 503:
       <br/>
       <br/>
-
       <table>
+
       <table style="border-radius: 30px;  background:cyan;  padding:10px 10px 10px 10px;">
-
       <th><tr><td><i>Erithromycin</i></td><td></td></tr></th>
+
       <th><tr><td style="background: #0099FF;"><b><font color="white">Erithromycin</font></b></td><td></td></tr></th>
       <tr>
       <tr>
         <td>Input times [min]</td>
         <td>Input times [min]</td>
-
         <td><input type="text" name="rg_start1" size="5" value="6000" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
+
         <td><input type="text" name="rg_start1" size="5" value="1500" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
-
         <td><input type="text" name="rg_start2" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
+
         <td><input type="text" name="rg_start2" size="5" value="10000" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
         <td><input type="text" name="rg_start3" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
         <td><input type="text" name="rg_start3" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
         <td><input type="text" name="rg_start4" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
         <td><input type="text" name="rg_start4" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
Line 503: Line 515:
       <tr>
       <tr>
         <td>Durations [min]</td>
         <td>Durations [min]</td>
-
         <td><input type="text" name="rg_duration1" size="5" value="1000" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
+
         <td><input type="text" name="rg_duration1" size="5" value="2000" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
-
         <td><input type="text" name="rg_duration2" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
+
         <td><input type="text" name="rg_duration2" size="5" value="100" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
         <td><input type="text" name="rg_duration3" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
         <td><input type="text" name="rg_duration3" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
         <td><input type="text" name="rg_duration4" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
         <td><input type="text" name="rg_duration4" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
Line 515: Line 527:
       <br />
       <br />
       <b>SIMULATION</b> <br/>
       <b>SIMULATION</b> <br/>
 +
      <hr />     
 +
      <input type="checkbox" name="noise" value="1" /> Apply measurement noise.
 +
      <br/>
 +
      <font color="blue">(Measured standard deviations will be applied in the calculations.)</font><br /> <br />
 +
-
      <hr />
 
       Time: <input type="text" name="time" size="5" value="15000" onKeyPress="return numbersonly(this, event)" maxlength="7"/> min<br />
       Time: <input type="text" name="time" size="5" value="15000" onKeyPress="return numbersonly(this, event)" maxlength="7"/> min<br />
       <font color="blue">(Simulation running time)</font><br /><br />
       <font color="blue">(Simulation running time)</font><br /><br />
-
      <input type="submit" value="SIMULATE" /> <br />
 
-
      <font color="blue">(The results will be shown in a new browser window/tab after few seconds. Have fun.)</font><br /><br />
 
-
 
-
    </form>
 
-
 
-
    <br />
 
-
   
 
-
    <h2><a name="model2"></a>Positive feedback loop switch</h2>
 
-
 
-
    <form name="form1" action="http://igem2012.fri.uni-lj.si:443/cellulator/bistable_feedback" target="_blank" method="GET">
 
-
      <input type="hidden" name="check_submit" value="1"/>
 
-
      <b>INPUT VECTORS DOSAGE</b>
 
        
        
-
 
+
       <input type="submit" value="SIMULATE" /><br/>
-
      <p>     
+
       <font color="blue">(The results will be shown in a new browser window/tab after few seconds.)</font>
-
      <!-- inline figure 1 -->
+
-
       <table class="inliner" style="width:50%;">
+
-
      <tbody  class="inliner">
+
-
       <tr class="inliner"><td class="inliner"><img class="inliner" src="https://static.igem.org/mediawiki/2012/a/a4/Svn12_interactive_scheme-02.png"/></td></tr>
+
-
      .</td></tr>
+
-
      </tbody>
+
-
      </table>
+
-
      <!-- end figure 1-->
+
        
        
-
       <table class="normal">
+
       </td>
-
        <thead class="normal">
+
-
        <tr class="normal"><td class="normal">Construct</td><td class="normal">Dosage</td></tr>
+
-
        </thead>
+
-
        <tbody class="normal">
+
-
        <tr class="normal"><td class="normal"><strong>[A]_pCMV_TAL-B:KRAB_TAL-A:VP16_BFP </strong></td><td class="normal"><input type="text" name="plasmid1" size="5" value="200" onKeyPress="return numbersonly(this, event)"/> ng</td></tr>
+
-
        <tr class="normal"><td class="normal"><strong>[B]_pCMV_TAL-A:KRAB_TAL-B:VP16_mCitrine</strong></td><td class="normal"><input type="text" name="plasmid2" size="5" value="200" onKeyPress="return numbersonly(this, event)"/> ng</td></tr>
+
-
        <tr class="normal"><td class="normal"><strong>pCMV_[PIR]_TAL-B:KRAB_TAL-A:VP16</strong></td><td class="normal"><input type="text" name="plasmid3" size="5" value="200" onKeyPress="return numbersonly(this, event)"/> ng</td></tr>
+
-
        <tr class="normal"><td class="normal"><strong>pCMV_[ETR]_TAL-A:KRAB_TAL-B:VP16</strong></td><td class="normal"><input type="text" name="plasmid4" size="5" value="200" onKeyPress="return numbersonly(this, event)"/> ng</td></tr>
+
-
        <tr class="normal"><td class="normal"><strong>pCMV_PIP:KRAB_E:KRAB</strong></td><td class="normal"><input type="text" name="plasmid5" size="5" value="200" onKeyPress="return numbersonly(this, event)"/> ng</td></tr>
+
-
        </tbody>
+
-
        </table>
+
-
      <font color="blue">(Enter dosages for corresponding plasmids.)</font><br /><br />
+
-
      </p>
+
-
      <div style="clear:both;"></div>
+
-
     
+
-
     
+
-
      <hr/>
+
-
      <b>TRANSCRIPTION FACTORS</b>
+
-
      <br />
+
-
      <input type="checkbox" name="req" value="1" /> Equal transcription factors <br />
+
-
      <font color="blue">(Transcription factors will alter transcription with equal rates)</font><br /><br />
+
-
      <hr/>
+
-
      <b>INDUCERS</b> <br/>
+
-
 
+
-
     
+
-
      <table>
+
-
      <th><tr><td><i>Pristinamycin</i></td><td></td></tr></th>
+
-
      <tr>
+
-
        <td>Input times [min]</td>
+
-
        <td><input type="text" name="pc_start1" size="5" value="7000" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
+
-
        <td><input type="text" name="pc_start2" size="5" value="1000" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
+
-
        <td><input type="text" name="pc_start3" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
+
-
        <td><input type="text" name="pc_start4" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
+
-
        <td><input type="text" name="pc_start5" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
+
-
      </tr>
+
-
      <tr>
+
-
        <td>Durations [min]</td>
+
-
        <td><input type="text" name="pc_duration1" size="5" value="1000" onKeyPress="return numbersonly(this, event)" maxlength="6"><br/></td>
+
-
        <td><input type="text" name="pc_duration2" size="5" value="1000" onKeyPress="return numbersonly(this, event)" maxlength="6"><br/></td>
+
-
        <td><input type="text" name="pc_duration3" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"><br/></td>
+
-
        <td><input type="text" name="pc_duration4" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"><br/></td>
+
-
        <td><input type="text" name="pc_duration5" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"><br/></td>
+
       </tr>
       </tr>
       </table>
       </table>
-
 
 
-
      <br/>
 
-
 
-
      <table>
 
-
      <th><tr><td><i>Erithromycin</i></td><td></td></tr></th>
 
-
      <tr>
 
-
        <td>Input times [min]</td>
 
-
        <td><input type="text" name="rm_start1" size="5" value="3000" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
 
-
        <td><input type="text" name="rm_start2" size="5" value="14000" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
 
-
        <td><input type="text" name="rm_start3" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
 
-
        <td><input type="text" name="rm_start4" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
 
-
        <td><input type="text" name="rm_start5" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"/></td>
 
-
      </tr>
 
-
      <tr>
 
-
        <td>Durations [min]</td>
 
-
        <td><input type="text" name="rm_duration1" size="5" value="1000" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
 
-
        <td><input type="text" name="rm_duration2" size="5" value="2000" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
 
-
        <td><input type="text" name="rm_duration3" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
 
-
        <td><input type="text" name="rm_duration4" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
 
-
        <td><input type="text" name="rm_duration5" size="5" value="" onKeyPress="return numbersonly(this, event)" maxlength="6"></td>
 
-
      </tr>
 
-
      </table>
 
-
      <font color="blue">(For each input time of an inducer, enter its corresponding duration, i.e. after how many minutes the inducer will be removed. )</font>
 
-
      <br />
 
-
      <br />
 
        
        
-
 
-
 
-
 
-
      <hr/>
 
-
      <b>SIMULATION</b> <br/>
 
-
      Time: <input type="text" name="time" size="5" value="20000"/> min<br />
 
-
      <font color="blue">(Simulation running time)</font><br />
 
-
      <br />
 
        
        
-
      <input type="submit" value="SIMULATE" /><br/>
 
-
      <font color="blue">(The results will be shown in a new browser window/tab after few seconds. Have fun.)</font>
 
     </form>  
     </form>  

Latest revision as of 21:08, 26 October 2012


Experimental model interactive simulations


Based on experimental data, we constructed an experimental model. Please see Experimental model for details of derivation. For old models (developed before European Regional Jamboree), click here.

INPUT VECTORS DOSAGE
The Switch
ConstructDosage
ng
ng
ng
ng
Inducible system
ConstructDosage
ng
ng
ng
ng
Pristinamycin/Erithromycin ind. proteins
ConstructDosage
ng
ng
(Enter dosages for corresponding plasmids. To comply with the jetPEI® protocol, the sum of masses shall not exceed 1000 ng. )

 INDUCERS
Pristinamycin
Input times [min]
Durations [min]





Erithromycin
Input times [min]
Durations [min]
(For each input time of an inducer, enter its corresponding duration, i.e. after how many minutes the inducer will be removed. )

SIMULATION
Apply measurement noise.
(Measured standard deviations will be applied in the calculations.)

Time: min
(Simulation running time)


(The results will be shown in a new browser window/tab after few seconds.)
Next: Parts >>

Retrieved from "http://2012.igem.org/Team:Slovenia/ModelingInteractiveSimulations"