Team:Slovenia/ModelingInteractiveSimulations

From 2012.igem.org

(Difference between revisions)
 
(20 intermediate revisions not shown)
Line 156: Line 156:
/* Tables */
/* Tables */
/* IE 6: http://webdesign.about.com/od/tables/qt/tiptablecenter.htm */
/* IE 6: http://webdesign.about.com/od/tables/qt/tiptablecenter.htm */
-
table.normal { border-collapse: collapse; margin: auto; width:80%; margin-bottom:15px; }
+
table.normal { border-collapse: collapse; margin: auto; width:70%; margin-bottom:15px; }
td.normal, th.normal { padding-left: 1.4em; padding-right: 1.4em; padding-top: 0.4em; padding-bottom: 0.4em; border: 1px #d8d8d8 solid; }
td.normal, th.normal { padding-left: 1.4em; padding-right: 1.4em; padding-top: 0.4em; padding-bottom: 0.4em; border: 1px #d8d8d8 solid; }
thead.normal{ background: #0C5DA5; color:#ffffff; border: 1px #d8d8d8 solid; }
thead.normal{ background: #0C5DA5; color:#ffffff; border: 1px #d8d8d8 solid; }
Line 212: Line 212:
#cssmenu ul li > ul li{display:block; list-style:inside none; padding:0; margin:0; position:relative;}  
#cssmenu ul li > ul li{display:block; list-style:inside none; padding:0; margin:0; position:relative;}  
#cssmenu ul li > ul li a{ outline:none; display:block; position:relative; margin:0; padding:8px 20px; font:10pt Arial, Helvetica, sans-serif; color:#fff; text-decoration:none; text-shadow:1px 1px 0 rgba(0,0,0, 0.5); }  
#cssmenu ul li > ul li a{ outline:none; display:block; position:relative; margin:0; padding:8px 20px; font:10pt Arial, Helvetica, sans-serif; color:#fff; text-decoration:none; text-shadow:1px 1px 0 rgba(0,0,0, 0.5); }  
 +
#cssmenu ul li > ul li a table tr td span{ outline:none; display:block; position:relative; margin:0; padding:0px 0px; font:10pt Arial, Helvetica, sans-serif; color:#fff; text-decoration:none; text-shadow:1px 1px 0 rgba(0,0,0, 0.5); }
#cssmenu, #cssmenu > ul > li > ul > li a:hover
#cssmenu, #cssmenu > ul > li > ul > li a:hover
{ background:#043A6B;  
{ background:#043A6B;  
Line 228: Line 229:
/* end CSS navigation menu (blue) */
/* end CSS navigation menu (blue) */
 +
/*new table start*/
 +
table.newtable {background-color:transparent;}
 +
td.newtable, th.newtable {background-color:transparent;}
 +
thead.newtable{ }
 +
tbody .newtable{}
 +
/*new table*/
ul {
ul {
Line 281: Line 288:
}  
}  
 +
</style>
</style>
Line 305: Line 313:
<div id="banner">
<div id="banner">
-
<a style="position:absolute; top:0px; left:490px;" href="https://2012.igem.org/Main_Page"><b>iGEM 2012</b></a>
 
</div>
</div>
Line 311: Line 318:
<!--<div id="container">-->
<!--<div id="container">-->
<div id="mainmenu">
<div id="mainmenu">
 +
<!-- start main menu -->
<!-- start main menu -->
Line 328: Line 336:
<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>
Line 336: Line 345:
<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>
Line 344: Line 353:
<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>
Line 351: Line 361:
  <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>
+
    <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>
Line 367: Line 377:
  <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>
+
    <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>
Line 390: Line 400:
<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>  
Line 397: Line 408:
</div>
</div>
<!-- end main menu -->
<!-- end main menu -->
 +
</div> <!-- end menu -->
</div> <!-- end menu -->
Line 404: Line 416:
 +
    <br/>
 +
    <h1>Experimental model interactive simulations </h1>
 +
    <br/>
-
<body>
 
-
    <br/>
+
 
-
    <h1>Quantitative model interactive simulations </h1>
+
<!-- dummy link na bannerju -->
-
    <br/>
+
<a href="https://2012.igem.org/Main_Page">
 +
<div id="dummy" style="background-color:transparent; position:absolute; left:870px; top:25px; width:115px; height:80px; z-index:100; opacity:0.0;">
 +
</div>
 +
</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>
 
-
 
-
    <h2><a name="model1"></a>Mutual repressor switch</h2>
 
      
      
-
     <form name="form1" action="http://igem2012.fri.uni-lj.si:443/cellulator/bistable" target="_blank" method="GET">
+
     <form name="form1" action="http://igem2012.fri.uni-lj.si:443/cellulator/bistable_feedback_new" method="GET" onsubmit="return validateForm(this)">
       <input type="hidden" name="check_submit" value="1"/>  
       <input type="hidden" name="check_submit" value="1"/>  
 +
   
 +
     
 +
 +
 +
      <table class="invisibile" style="border-radius: 30px;  background:cyan;  padding:10px 10px 10px 10px;">
 +
      <tr class="invisibile">
 +
     
 +
      <td class="invisibile" width="700px" valign="top">
 +
     
       <b>INPUT VECTORS DOSAGE</b> <br/>
       <b>INPUT VECTORS DOSAGE</b> <br/>
 +
      <hr/>
        
        
-
       <table>
+
       <table style="border-radius: 30px;  background:cyan;  padding:10px 10px 10px 10px;" width="95%">
-
        <th>
+
      <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>
         <tr><td>Construct</td><td>Dosage</td></tr>
         </th>
         </th>
-
       <tr><td><strong>[A]_pCMV_TAL-B:KRAB_BFP</strong> </td><td> <input type="text" name="plasmid1" size="5" value="190" onKeyPress="return numbersonly(this, event)" maxlength="4"/> ng</td></tr>
+
       <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><strong>[B]_pCMV_TAL-A:KRAB_mCitrine</strong> </td><td> <input type="text" name="plasmid2" size="5" value="180" onKeyPress="return numbersonly(this, event)" maxlength="4"/> 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><strong>pCMV_[PIR]_TAL-B:KRAB</strong> </td><td> <input type="text" name="plasmid3" size="5" value="190" onKeyPress="return numbersonly(this, event)" maxlength="4"/> 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><strong>pCMV_[ETR]_TAL-B:KRAB</strong> </td><td> <input type="text" name="plasmid4" size="5" value="180" onKeyPress="return numbersonly(this, event)" maxlength="4"/> 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><strong>pCMV_PIP:KRAB</strong> </td><td> <input type="text" name="plasmid5" size="5" value="180" onKeyPress="return numbersonly(this, event)" maxlength="4"/> ng</td></tr>
+
      <tr><td></td><td></td></tr>
-
       <tr><td><strong>pCMV_E:KRAB </strong> </td><td> <input type="text" name="plasmid6" size="5" value="180" onKeyPress="return numbersonly(this, event)" maxlength="4"/> ng</td></tr>
+
        
 +
      <th><tr><td style="background: #0099FF;"><b><font color="white">Inducible system</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/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>
       </table>
-
       <font color="red">(Enter dosages for corresponding plasmids.)</font><br /><br />
+
       <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="red">(Transcription factors will alter transcription with equal rates)</font><br /> <br />
 
-
     
 
-
      <hr/>
 
-
      <b>INDUCERS</b> <br/>
 
        
        
-
       <table>
+
       <table style="border-radius: 30px;  background:cyan;  padding:10px 10px 10px 10px;">
-
      <th><tr><td><i>Pristinamycin</i></td><td></td></tr></th>
+
        <th><tr><td style="background: #0099FF;"><b><font color="white">Pristinamycin</font></b></td><td></td></tr></th>
       <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 464: 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 474: 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 486: 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 494: Line 523:
       </table>
       </table>
        
        
-
       <font color="red">(For each input time of an inducer, enter its corresponding duration, i.e. after how many minutes the inducer will be removed. )</font><br />
+
       <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 />
       <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="red">(Simulation running time)</font><br /><br />
+
       <font color="blue">(Simulation running time)</font><br /><br />
-
      <input type="submit" value="SIMULATE" /> <br /><br /><br />
 
-
      <font color="red">(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>
 
        
        
-
       <table>
+
       <input type="submit" value="SIMULATE" /><br/>
-
        <th>
+
       <font color="blue">(The results will be shown in a new browser window/tab after few seconds.)</font>
-
        <tr><td>Construct</td><td>Dosage</td></tr>
+
-
        </th>
+
-
        <tr><td><strong>[A]_pCMV_TAL-B:KRAB_TAL-A:VP16_BFP </strong></td><td><input type="text" name="plasmid1" size="5" value="200" onKeyPress="return numbersonly(this, event)"/> ng</td></tr>
+
-
        <tr><td><strong>[B]_pCMV_TAL-A:KRAB_TAL-B:VP16_mCitrine</strong></td><td><input type="text" name="plasmid2" size="5" value="200" onKeyPress="return numbersonly(this, event)"/> ng</td></tr>
+
-
        <tr><td><strong>pCMV_[PIR]_TAL-B:KRAB_TAL-A:VP16</strong></td><td><input type="text" name="plasmid3" size="5" value="200" onKeyPress="return numbersonly(this, event)"/> ng</td></tr>
+
-
        <tr><td><strong>pCMV_[ETR]_TAL-A:KRAB_TAL-B:VP16</strong></td><td><input type="text" name="plasmid4" size="5" value="200" onKeyPress="return numbersonly(this, event)"/> ng</td></tr>
+
-
        <tr><td><strong>pCMV_PIP:KRAB_E:KRAB</strong></td><td><input type="text" name="plasmid5" size="5" value="200" onKeyPress="return numbersonly(this, event)"/> ng</td></tr>
+
-
       </table>
+
-
      <font color="red">(Enter dosages for corresponding plasmids.)</font><br /><br />
+
        
        
-
       <hr/>
+
       </td>
-
      <b>TRANSCRIPTION FACTORS</b>
+
-
      <br />
+
-
      <input type="checkbox" name="req" value="1" /> Equal transcription factors <br />
+
-
      <font color="red">(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="red">(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="red">(Simulation running time)</font><br />
 
-
      <br />
 
        
        
-
      <input type="submit" value="SIMULATE" />
 
-
      <font color="red">(The results will be shown in a new browser window/tab after few seconds. Have fun.)</font>
 
     </form>  
     </form>  
 +
 +
<hr>
 +
<b>
 +
Next: <a href='https://2012.igem.org/Team:Slovenia/Parts'>Parts >></a>
 +
</b>

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 >>