Team:Aberdeen Scotland/Modeling

From 2014.igem.org

(Difference between revisions)
(Prototype team page)
 
(19 intermediate revisions not shown)
Line 1: Line 1:
-
<!-- *** What falls between these lines is the Alert Box!  You can remove it from your pages once you have read and understood the alert *** -->
 
-
 
-
 
-
{{CSS/Main}}
 
-
 
-
 
<html>
<html>
 +
<head>
-
<!--main content -->
+
<!-- Charset -->
-
<table width="70%" align="center">
+
<meta charset="UTF-8">
-
 
+
-
 
+
<title>Team:Aberdeen Scotland/Modelling - 2014.ogem.org</title>
-
<!--welcome box -->
+
-
<tr>
+
-
<td style="border:1px solid black;" colspan="3" align="center" height="150px" bgColor=#FF404B>
+
-
<h1 >WELCOME TO iGEM 2014! </h1>
+
-
<p>Your team has been approved and you are ready to start the iGEM season!
+
-
<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
+
-
<br>
+
-
<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:Aberdeen_Scotland/Modeling&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
+
-
</td>
+
-
</tr>
+
-
 
+
-
<tr> <td colspan="3"  height="5px"> </td></tr>
+
-
<!-- end welcome box -->
+
-
<tr>
+
-
 
+
-
<!--navigation menu -->
+
-
<td align="center" colspan="3">
+
-
 
+
-
<table  width="100%">
+
-
<tr heigth="15px"></tr>
+
-
<tr heigth="75px">
+
-
 
+
-
 
+
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
+
-
<a href="https://2014.igem.org/Team:Aberdeen_Scotland"style="color:#000000">Home </a> </td>
+
-
 
+
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
-
<a href="https://2014.igem.org/Team:Aberdeen_Scotland/Team"style="color:#000000"> Team </a> </td>
+
-
 
+
-
<td style="border:1px solid black;" align="center"  height ="45px"  onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
-
<a href="https://igem.org/Team.cgi?year=2014&team_name=Aberdeen_Scotland"style="color:#000000"> Official Team Profile </a></td>
+
-
 
+
-
<td style="border:1px solid black" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
+
-
<a href="https://2014.igem.org/Team:Aberdeen_Scotland/Project"style="color:#000000"> Project</a></td>
+
-
 
+
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
-
<a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts"style="color:#000000"> Parts</a></td>
+
-
 
+
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
-
<a href="https://2014.igem.org/Team:Aberdeen_Scotland/Modeling"style="color:#000000"> Modeling</a></td>
+
-
 
+
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
+
-
<a href="https://2014.igem.org/Team:Aberdeen_Scotland/Notebook"style="color:#000000"> Notebook</a></td>
+
-
 
+
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
-
<a href="https://2014.igem.org/Team:Aberdeen_Scotland/Safety"style=" color:#000000"> Safety </a></td>
+
-
 
+
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
-
<a href="https://2014.igem.org/Team:Aberdeen_Scotland/Attributions"style="color:#000000"> Attributions </a></td>
+
 +
<!-- JavaScript -->
 +
<script src="https://2014.igem.org/Template:Team:Aberdeen_Scotland/JS?action=raw&ctype=text/js"></script>
-
<td align ="center"> <a href="https://2014.igem.org/Main_Page"> <img src="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png" width="55px"></a> </td>
+
<!-- Include CSS -->
-
</tr>
+
<link rel="stylesheet" type="text/css" href="https://2014.igem.org/Template:Team:Aberdeen_Scotland/CSS?action=raw&ctype=text/css">
-
</table>
+
-
</tr>
+
-
</tr>
+
-
</td>
+
 +
<!-- Include MathJax -->
 +
<script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-
<tr> <td colspan="3" height="15px"> </td></tr>
+
</head>
-
<tr><td bgColor="#e7e7e7" colspan="3" height="1px"> </tr>
+
<body>
-
<tr> <td colspan="3" height="5px"> </td></tr>
+
<div id="wrapper">
 +
<div id="header">
 +
<div class="logo">
 +
<a href="http://abdn.ac.uk" title="University of Aberdeen"></a>
 +
</div>
 +
<div id="navbar">
 +
<ul class="navbar">
 +
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland">Home</a></li>
 +
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Team">Team</a></li>
 +
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Project">Project</a></li>
 +
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Parts">Parts</a></li>
 +
<li><a class="Act" href="https://2014.igem.org/Team:Aberdeen_Scotland/Modeling">Modelling</a></li>
 +
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Notebook">Notebook</a></li>
 +
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Safety">Safety</a></li>
 +
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Attributions">Attributions</a></li>
 +
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Ethics">Ethics & Outreach</a></li>
 +
</ul>
 +
<div id="social">
 +
<ul class="social">
 +
<li><a href="http://twitter.com/iGEM2014ABDN" title="Twitter"><img src="https://static.igem.org/mediawiki/2014/7/78/Tw_inv_22.png"></a></li>
 +
<li><a href="http://plus.google.com/106825238674841642988" rel="publisher" title="Google+"><img src="https://static.igem.org/mediawiki/2014/4/45/G%2B22.png"></a></li>
 +
<li><a href="http://www.facebook.com/iGEM2014ABDN" title="Facebook"><img src="https://static.igem.org/mediawiki/2014/3/35/Fb_icon_22.png"></a></li>
 +
</ul>
 +
</div>
 +
</div>
 +
</div> <br class="clear"> <!-- END OF HEADER -->
 +
 +
<div id="pcontent">
 +
<br class="clear">
 +
<!-- SIDEBAR -->
 +
<div id="sidebar">
 +
<ul class="sidebar">
 +
<li class="curr"><a class="curr" href="https://2014.igem.org/Team:Aberdeen_Scotland/Modeling">Introduction</a></li>
 +
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Modeling/QS">Quorum Sensing</a></li>
 +
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Modeling/GFP">GFP Response</a></li>
 +
<li><a href="https://2014.igem.org/Team:Aberdeen_Scotland/Modeling/Assay">Assay Sensitivity</a></li>
 +
</ul>
 +
</div>
-
<!--modeling content -->
+
<!-- CONTAINER -->
-
<tr><td colspan="3"> <h3>Modeling</h3></td></tr>
+
<div id="container">
-
</tr>
+
 +
<!-- SECTION HEAD -->
 +
<div class="t_overview">
 +
<h1>Modelling Aims</h1>
 +
<!-- <h3></h3> -->
 +
</div> <br class="clear"> <!-- END OF HEAD -->
 +
 +
<!-- PAGE CONTENT -->
 +
<div class="main_content">
 +
<h3>Purpose</h3>
 +
<p></p>
 +
<p>In order to verify and characterize our diagnostic system we created mathematical models for each individual component. Modeling and simulations were essential
 +
techniques that guided our approach from design to completion. As the main point of interest in our system was inter-cellular communication and its optimization, we
 +
employed ODEs and PDEs as our main mathematical tools.</p>
 +
<img src="https://static.igem.org/mediawiki/2014/a/a7/AjkIkdjfmkJ.png">
 +
<h3>Quorum Sensing</h3>
 +
<p>We developed a spacial model for analyzing Quorum Sensing between cells and then studied it under our system desired conditions. This gave us insight into how
 +
best structure our assay.</p>
 +
<h3>GFP Response</h3>
 +
<p>By simulating GFP response we made sure our system will react in a predictable manner and in an appropriate amount of time. We ensured that simulations agreed with
 +
data so that we can rely on reproducibility.</p>
 +
<h3>Assay Sensitivity</h3>
 +
<p>As with any other test, sensitivity is a main factor. The test needed to be sensitive enough to detect HAT, but also tolerant to noise, so that false-positives
 +
were minimized. We explored the process of antibody binding to make sure we meet those criteria.</p>
 +
</div> <br class="clear"> <!-- END OF PAGE CONTENT -->
-
<tr>
+
</div> <!-- END OF CONTAINER -->
-
<td width="45%"  valign="top">  
+
-
<p>If you choose to create a model during your project, please write about it here. Modeling is not an essential part of iGEM, but we encourage any and all teams to model some aspect of their project. See previous "Best Model" awards for more information.</p>
+
</div> <br class="clear"> <!-- END OF PAGE CONTENT -->
-
</td>
+
-
<td></td>
+
<div id="footer">
-
<td></td>
+
-
</tr>
+
 +
<ul class="sponsors">
 +
<li><a href="http://www.abdn.ac.uk/" title="University of Aberdeen"><img src="https://static.igem.org/mediawiki/2014/c/c6/Uni_of_ab.png"></a></li>
 +
<li><a href="http://www.bbsrc.ac.uk/" title="BBSRC"><img src="https://static.igem.org/mediawiki/2014/a/a9/Bbsrc.png"></a></li>
 +
<li><a href="http://www.biochemistry.org" title="Biochemical Society"><img src="https://static.igem.org/mediawiki/2014/7/7c/Biochem_soc.png"></a></li>
 +
<li><a href="http://www.sgm.ac.uk/" title="Society for General Microbiology"><img src="https://static.igem.org/mediawiki/2014/f/f5/Soc_general_microb.png"></a></li>
 +
<li><a href="http://www.sulsa.ac.uk/" title="SULSA"><img src="https://static.igem.org/mediawiki/2014/2/24/Sulsa.png"></a></li>
 +
</ul>
-
</table>
+
</div> <!-- END OF FOOTER -->
 +
</div> <!-- END OF PAGE WRAPPER-->
 +
</body>
</html>
</html>

Latest revision as of 02:20, 18 October 2014

Team:Aberdeen Scotland/Modelling - 2014.ogem.org



Modelling Aims


Purpose

In order to verify and characterize our diagnostic system we created mathematical models for each individual component. Modeling and simulations were essential techniques that guided our approach from design to completion. As the main point of interest in our system was inter-cellular communication and its optimization, we employed ODEs and PDEs as our main mathematical tools.

Quorum Sensing

We developed a spacial model for analyzing Quorum Sensing between cells and then studied it under our system desired conditions. This gave us insight into how best structure our assay.

GFP Response

By simulating GFP response we made sure our system will react in a predictable manner and in an appropriate amount of time. We ensured that simulations agreed with data so that we can rely on reproducibility.

Assay Sensitivity

As with any other test, sensitivity is a main factor. The test needed to be sensitive enough to detect HAT, but also tolerant to noise, so that false-positives were minimized. We explored the process of antibody binding to make sure we meet those criteria.