Team:Edinburgh/modelling(overalldescription)

From 2009.igem.org

(Difference between revisions)
 
(25 intermediate revisions not shown)
Line 88: Line 88:
border-top:6px solid #CA9A38;
border-top:6px solid #CA9A38;
border-bottom:6px solid #CA9A38;
border-bottom:6px solid #CA9A38;
 +
}
 +
 +
#Upgradebox {
 +
background-color:#dae7b4;
 +
        float:left;
 +
width:150px;
 +
margin-top:320px;
 +
        border-top:6px solid #CA9A38;
 +
        border-bottom:6px solid #CA9A38;
 +
        font-size:11px;
 +
        font-family:Arial;
 +
        color:#556B2F;
 +
}
 +
 +
#Upgradenote {
 +
padding:5%;
}
}
Line 98: Line 114:
#contentmenu {
#contentmenu {
         margin-bottom:30px;
         margin-bottom:30px;
-
         margin-left:191px;
+
         margin-left:251px;
text-decoration: none
text-decoration: none
}
}
Line 107: Line 123:
         margin-bottom:2px;
         margin-bottom:2px;
background-color: #e5e7e2;
background-color: #e5e7e2;
-
height:1050px;
+
height:650px;
         width:795px;
         width:795px;
-
         font-size:11px;
+
         font-size:12px;
         text-align:justify;
         text-align:justify;
}
}
Line 142: Line 158:
#nav {
#nav {
-
     width: 690px;
+
     width: 750px;
}
}
Line 183: Line 199:
<div id=main>
<div id=main>
<div id=leftspace>
<div id=leftspace>
 +
                  <div id="Upgradebox">
 +
            <div id="Upgradenote" align="left">
 +
                      Our WIKI is best viewed with (click title):<br /><br />
 +
                      * <a target="_blank" style="color:#00008B;text-decoration:underline;" href="http://www.microsoft.com/windows/Internet-explorer/default.aspx">Internet Explorer 8</a> <br />
 +
                      * <a target="_blank" style="color:#00008B;text-decoration:underline;" href="http://www.mozilla.com/en-US/">Firefox 3</a><br />
 +
                      * <a target="_blank" style="color:#00008B;text-decoration:underline;" href="http://get.adobe.com/flashplayer/">Adobe Flash Player 10</a> <br /><br />
 +
                      If you encounter any visual problems please upgrade your browser to the latest version in order to get the most out of our WIKI. Thank you!
 +
                    </div>
 +
                  </div>
</div>
</div>
<div id=mainmenu>
<div id=mainmenu>
-
<div id=menuitem >  <a href="#"> Overall description </a> </div>  
+
<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/modelling%28overalldescription%29"> Overall description </a> </div>  
-
<div id=menuitem >  <a href="#"> Gene regulatory network </a> </div>  
+
<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/modelling%28generegulatorynetwork%29"> Gene regulatory network </a> </div>  
-
<div id=menuitem >  <a href="#"> Real life modelling </a> </div>
+
<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/modelling%28reallifemodelling%29"> Real life modelling </a> </div>
-
<div id=menuitem >  <a href="#"> Results </a> </div>
+
                        <div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/reallifeapplication%28scaleup%29"> Scale Up </a> </div>
-
<div id=menuitem >  <a href="#"> Glance at the future </a> </div>
+
<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/modelling%28results%29"> Results </a> </div>
-
<div id=menuitem >  <a href="#"> References </a> </div>
+
<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/modelling%28references%29"> References </a> </div>
</div>
</div>
<div id=Edinburghcontainer>
<div id=Edinburghcontainer>
Line 196: Line 221:
<ul id="nav" class="dropdown dropdown-horizontal">
<ul id="nav" class="dropdown dropdown-horizontal">
  <li><a href="https://2009.igem.org/Team:Edinburgh">Home</a></li>
  <li><a href="https://2009.igem.org/Team:Edinburgh">Home</a></li>
-
 
-
<li><a href="https://2009.igem.org/Team:Edinburgh/projectmain%28overall%29" class="dir">Top View</a>
 
-
  <ul>
 
-
  <li><a href="https://2009.igem.org/Team:Edinburgh/projectmain%28overall%29">Overall Description</a></li>
 
-
  <li><a href="https://2009.igem.org/Team:Edinburgh/projectmain%28motivationl%29">Motivation</a></li>
 
-
  <li><a href="https://2009.igem.org/Team:Edinburgh/projectmain%28whywediffer%29">Why We Differ?</a></li>
 
-
  <li><a href="https://2009.igem.org/Team:Edinburgh/projectmain%28glanceatthefuture%29">Glance At The Future</a></li>
 
-
  <li><a href="https://2009.igem.org/Team:Edinburgh/projectmain%28references%29">References</a></li>
 
-
  </ul>
 
-
  </li>
 
   <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28overalldescription%29" class="dir">Biology</a>
   <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28overalldescription%29" class="dir">Biology</a>
   <ul>
   <ul>
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28overalldescription%29">Overall Description and Design</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28overalldescription%29">Overall Description and Design</a></li>
-
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28materialsandmethods%29">Materials and Methods</a></li>
+
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28tntsensing%29">TNT-Sensing Pathway</a></li>
-
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28biobricks%29">Biobricks</a></li>
+
    <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28nitritenitratesensing%29">Nitrite/Nitrate-Sensing Pathway</a></li>
 +
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28biobricks%29">Biobrick Parts</a></li>
 +
    <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28results%29">Results</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28solvedproblems%29">Problem Solving and Tips</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28solvedproblems%29">Problem Solving and Tips</a></li>
-
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28results%29">Results</a></li>
+
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28materialsandmethods%29">Materials and Methods</a></li>
-
    <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28glanceatthefuture%29">Future Work</a></li>
+
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28references%29">References</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28references%29">References</a></li>
   </ul>
   </ul>
Line 226: Line 242:
     <li><a href="https://2009.igem.org/Team:Edinburgh/reallifeapplication%28scaleup%29">Scale Up</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/reallifeapplication%28scaleup%29">Scale Up</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/modelling%28results%29">Results</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/modelling%28results%29">Results</a></li>
-
    <li><a href="https://2009.igem.org/Team:Edinburgh/modelling%28glanceatthefuture%29">Glance At the Future</a></li>
 
     <li><a href="https://2009.igem.org/Team:Edinburgh/modelling%28references%29">References</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/modelling%28references%29">References</a></li>
   </ul>
   </ul>
   </li>
   </li>
-
   <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28introduction%29" class="dir">Underlying Philosophy</a>
+
   <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28publicperception%29" class="dir">Underlying Philosophy</a>
     <ul>
     <ul>
-
     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28introduction%29">Introduction</a></li>
+
     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28publicperception%29">Public Perception</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28legislationissues%29">Legislation issues</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28legislationissues%29">Legislation issues</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28biosafety%29">Biosafety</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28biosafety%29">Biosafety</a></li>
-
    <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28religiousperception%29">Religious Perception</a></li>
+
     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28summary%29">DEMOCS Card Game</a></li>
-
    <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28publicperception%29">Public Perception</a></li>
+
-
    <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28surveyandconclusions%29">Survey and Conclusions</a></li>
+
-
     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28summary%29">Summary (Synthetic Bilogy Pro and Contras)</a></li>
+
     </ul>
     </ul>
   </li>
   </li>
-
   <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28introduction%29" class="dir">New Informatics</a>
+
   <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28introduction%29" class="dir">Informatics</a>
     <ul>
     <ul>
       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28introduction%29">Introduction</a></li>
       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28introduction%29">Introduction</a></li>
-
      <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28conceptsandtechnology%29">Concepts and Technologies</a></li>
 
       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28globetutorial%29">Globe Tutorial</a></li>
       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28globetutorial%29">Globe Tutorial</a></li>
       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28igemwikhacks%29">iGEM WIKI Hacks</a></li>
       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28igemwikhacks%29">iGEM WIKI Hacks</a></li>
-
       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28conclusions%29">Conclusions</a></li>
+
       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28conclusions%29">Blog Entry</a></li>
     </ul>
     </ul>
   </li>
   </li>
-
 
+
 
-
  <li><a href="https://2009.igem.org/Team:Edinburgh/results">Results</a></li>
+
   <li><a href="https://2009.igem.org/Team:Edinburgh/Notebook">Notebook</a></li>
   <li><a href="https://2009.igem.org/Team:Edinburgh/Notebook">Notebook</a></li>
    
    
-
   <li><a href="https://2009.igem.org/Team:Edinburgh/team%28teamintroduction%29" class="dir">Team</a>
+
   <li><a href="https://2009.igem.org/Team:Edinburgh/team%28teammembers%29" class="dir">Team</a>
   <ul>
   <ul>
-
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28teamintroduction%29">Team Introduction</a></li>
 
-
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28edinburghuniversity%29">Edinburgh University</a></li>
 
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28teammembers%29">Team Members</a></li>
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28teammembers%29">Team Members</a></li>
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28advisors%29">Advisors</a></li>
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28advisors%29">Advisors</a></li>
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28supervisors%29">Supervisors</a></li>
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28supervisors%29">Supervisors</a></li>
-
        <li><a href="https://2009.igem.org/Team:Edinburgh/team%28our message%29">Our Message</a></li>
 
         <li><a href="https://2009.igem.org/Team:Edinburgh/team%28gallery%29">Gallery</a></li>
         <li><a href="https://2009.igem.org/Team:Edinburgh/team%28gallery%29">Gallery</a></li>
         <li><a href="https://2009.igem.org/Team:Edinburgh/team%28contacts%29">Contacts</a></li>
         <li><a href="https://2009.igem.org/Team:Edinburgh/team%28contacts%29">Contacts</a></li>
Line 271: Line 278:
</ul>
</ul>
         </div>
         </div>
-
<font color="#323131" style="font-size:14px;float:left;margin-left:20px;margin-top:20px;"><b>Overall description</b></font>
+
<font color="#323131" style="font-size:14px;float:left;margin-left:20px;margin-top:20px;"><b>Modelling - Overall Description</b></font>
<div id=Edinburghcontent>
<div id=Edinburghcontent>
Line 278: Line 285:
<div id="abstarct" style="background-color:#e4f5ca;border:1px solid #595151;width:755px;height:220px;margin-top:10px;margin-left:20px;font-size:11px;text-align:justify;padding-left:5px;padding-right:5px;padding-top:5px;padding-bottom:5px;">
<div id="abstarct" style="background-color:#e4f5ca;border:1px solid #595151;width:755px;height:220px;margin-top:10px;margin-left:20px;font-size:11px;text-align:justify;padding-left:5px;padding-right:5px;padding-top:5px;padding-bottom:5px;">
-
<b> Abstract </b> <br /><br />
+
<b> Personal note </b> <br /><br />
-
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent nec nisi nec elit volutpat sollicitudin. Sed cursus venenatis egestas. In mollis vehicula dictum. Sed id lacus vitae tortor commodo pharetra porttitor ut purus. Nullam euismod urna at felis accumsan sit amet viverra leo fermentum. Phasellus ac molestie sapien. In in neque purus. Cras eget lorem arcu. Aliquam ornare tellus vel nisi commodo molestie. Aliquam aliquet magna nisl. Quisque velit nulla, adipiscing ut sagittis id, luctus viverra leo. Nam nunc nisl, euismod eu dignissim nec, eleifend ut augue. Phasellus tempor condimentum ipsum, ut molestie lorem suscipit vel. Nulla luctus turpis eget neque facilisis eget sodales ante tincidunt. Praesent congue lobortis mollis. Maecenas non augue id mi dignissim luctus. Donec quis volutpat lectus. Mauris condimentum sodales luctus.
+
I have never heard about the term ‘Synthetic Biology’ and the competition ‘iGEM’ until one day I received this email to recruit engineers. As I was hunting for something productive to do for the summer, and having had a strong interest in medicine and biology, I instantly applied for it. GREAT! Few days later, I joined the team, not knowing what the hell I was going to be working on.
 +
<br /><br />
 +
Since then, I have learnt a lot more about biological systems, and ways to model them. Synthetic biology really is an AMAZING branch of research. The things you can design bacteria to do are limitless and will be never ending. iGEM has been a great way of self teaching, and motivation while working in a inter-disciplinary undergraduate team. I look forward to hearing about outstanding breakthroughs from ‘Synthetic Biology’ in the future.
 +
<br /><br />
 +
<font color="green" style="float:right"> WinHo </font>
-
Nulla nec mauris sapien, eget gravida quam. Fusce vulputate risus eget diam elementum vel mattis nisi sagittis. Vivamus eget enim a nisl imperdiet aliquet commodo eget turpis. Aliquam nec mi ac neque tincidunt facilisis fringilla at sapien. Praesent in justo vel turpis hendrerit suscipit. Nullam nec magna leo, sed vulputate quam. Aliquam sollicitudin hendrerit erat at eleifend. Vivamus tincidunt felis vitae metus suscipit non volutpat neque tempus. Phasellus sagittis accumsan tellus, vitae pharetra ligula rhoncus vitae.
 
</div>
</div>
-
<img src="https://static.igem.org/mediawiki/2009/3/3b/EdinburghParagraphMarker.jpg" style="margin-left:-5px;margin-top:20px;">
+
<img src="https://static.igem.org/mediawiki/2009/1/1d/ModellingOverallDescrption.jpg" style="margin-left:-5px;margin-top:20px;">
<div id="text" style="margin-left:20px;margin-top:10px;padding-bottom:15px;">
<div id="text" style="margin-left:20px;margin-top:10px;padding-bottom:15px;">
-
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent nec nisi nec elit volutpat sollicitudin. Sed cursus venenatis egestas. In mollis vehicula dictum. Sed id lacus vitae tortor commodo pharetra porttitor ut purus. Nullam euismod urna at felis accumsan sit amet viverra leo fermentum. Phasellus ac molestie sapien. In in neque purus. Cras eget lorem arcu. Aliquam ornare tellus vel nisi commodo molestie. Aliquam aliquet magna nisl. Quisque velit nulla, adipiscing ut sagittis id, luctus viverra leo. Nam nunc nisl, euismod eu dignissim nec, eleifend ut augue. Phasellus tempor condimentum ipsum, ut molestie lorem suscipit vel. Nulla luctus turpis eget neque facilisis eget sodales ante tincidunt. Praesent congue lobortis mollis. Maecenas non augue id mi dignissim luctus. Donec quis volutpat lectus. Mauris condimentum sodales luctus.
+
Our system requires a lot of components to function properly, so we decided the aim of our modelling would be to model different setups on how it should be put together, and pick the best one suited to the task of our biosensor. This is a cheap way of doing things, and can be done many times. This arrangement would then be made in the wet lab if time allowed.
-
 
+
<br /><br />
-
Nulla nec mauris sapien, eget gravida quam. Fusce vulputate risus eget diam elementum vel mattis nisi sagittis. Vivamus eget enim a nisl imperdiet aliquet commodo eget turpis. Aliquam nec mi ac neque tincidunt facilisis fringilla at sapien. Praesent in justo vel turpis hendrerit suscipit. Nullam nec magna leo, sed vulputate quam. Aliquam sollicitudin hendrerit erat at eleifend. Vivamus tincidunt felis vitae metus suscipit non volutpat neque tempus. Phasellus sagittis accumsan tellus, vitae pharetra ligula rhoncus vitae.
+
We thought we would do something different this year from the traditional ordinary differential equations type modelling. The disadvantage of a model based on systems of differential equations is the necessity to enumerate every potential molecular species that could arise in the modelled system. Rule-based modelling on the other hand is much simpler. It describes biological interactions in terms of rules without the need to make presumptive choices about which terms to exclude from the model for simplification.
 +
<br /><br />
 +
The modelling software we used is <a href="http://www.cellucidate.com">Cellucidate</a> (Kappa language), an advanced, web-based platform for biological modelling. In Cellucidate, the molecular components of the cell are ‘agents’. These have sites that can undergo changes of state and can bind to the sites of other agents, as defined by the set of ‘rules’ that describe all of the permissible interactions between them. The dynamic behaviour of the modelled system can then be explored by executing the model using Cellucidate's stochastic simulator. The state of every agent in the system and every rule based events are observables, making the model easily understood.
 +
More details of this can be found <a href="https://2009.igem.org/Team:Edinburgh/modelling(generegulatorynetwork)">here</a>.
<br /><br />
<br /><br />
-
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent nec nisi nec elit volutpat sollicitudin. Sed cursus venenatis egestas. In mollis vehicula dictum. Sed id lacus vitae tortor commodo pharetra porttitor ut purus. Nullam euismod urna at felis accumsan sit amet viverra leo fermentum. Phasellus ac molestie sapien. In in neque purus. Cras eget lorem arcu. Aliquam ornare tellus vel nisi commodo molestie. Aliquam aliquet magna nisl. Quisque velit nulla, adipiscing ut sagittis id, luctus viverra leo. Nam nunc nisl, euismod eu dignissim nec, eleifend ut augue. Phasellus tempor condimentum ipsum, ut molestie lorem suscipit vel. Nulla luctus turpis eget neque facilisis eget sodales ante tincidunt. Praesent congue lobortis mollis. Maecenas non augue id mi dignissim luctus. Donec quis volutpat lectus. Mauris condimentum sodales luctus.
+
In addition to this, we also did some modelling of how the system would operate in real life which can be found <a href="https://2009.igem.org/Team:Edinburgh/modelling(reallifemodelling)">here</a>.
-
 
+
-
Nulla nec mauris sapien, eget gravida quam. Fusce vulputate risus eget diam elementum vel mattis nisi sagittis. Vivamus eget enim a nisl imperdiet aliquet commodo eget turpis. Aliquam nec mi ac neque tincidunt facilisis fringilla at sapien. Praesent in justo vel turpis hendrerit suscipit. Nullam nec magna leo, sed vulputate quam. Aliquam sollicitudin hendrerit erat at eleifend. Vivamus tincidunt felis vitae metus suscipit non volutpat neque tempus. Phasellus sagittis accumsan tellus, vitae pharetra ligula rhoncus vitae.
+
-
 
+
<br /><br />
<br /><br />
-
 
-
<div id="left" style="width:50%">
 
-
Here lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent nec nisi nec elit volutpat sollicitudin. Sed cursus venenatis egestas. In mollis vehicula dictum. Sed id lacus vitae tortor commodo pharetra porttitor ut purus. Nullam euismod urna at felis accumsan sit amet viverra leo fermentum. Phasellus ac molestie sapien. In in neque purus. Cras eget lorem arcu. Aliquam ornare tellus vel nisi commodo molestie. Aliquam aliquet magna nisl. Quisque velit nulla, adipiscing ut sagittis id, luctus viverra leo. Nam nunc nisl, euismod eu dignissim nec, eleifend ut augue. Phasellus tempor condimentum ipsum, ut molestie lorem suscipit vel. Nulla luctus turpis eget neque facilisis eget sodales ante tincidunt. Praesent congue lobortis mollis. Maecenas non augue id mi dignissim luctus. Donec quis volutpat lectus. Mauris condimentum sodales luctus. Cras eget lorem arcu. Aliquam ornare tellus vel nisi commodo molestie. Aliquam aliquet magna nisl. Quisque velit nulla, adipiscing ut sagittis id, luctus viverra leo. Donec quis volutpat lectus. Mauris condimentum sodales luctus. Cras eget lorem arcu. Aliquam ornare tellus vel nisi commodo molestie. Aliquam aliquet magna nisl. Quisque velit nulla, adipiscing ut sagittis id, luctus viverra leo.
 
</div>
</div>
-
 
-
<div id="right" style="width:49%">
 
-
 
-
<img src="http://www.scharfphoto.com/fine_art_prints/archives/199812-026-Staph-Bacteria.jpg" style="margin-left:10px;"width="370" height="300">
 
-
 
-
</div>
 
-
</div>
 
-
 
-
<div id=bottomlinks align=right>
 
-
<div id=link><a href=#>next page</a></div>
 
-
<div id=link><a href=#>previous page</a></div>
 
-
</div>
 
</div>
</div>
<div id=bottombox>
<div id=bottombox>
<div id=bottomboxtext align=center>
<div id=bottomboxtext align=center>
-
<font size=2>Edinburgh University iGem Team 2009</font>
+
<font size=2>Edinburgh University iGEM Team 2009</font>
</div>
</div>
</div>
</div>

Latest revision as of 23:04, 21 October 2009

Our WIKI is best viewed with (click title):

* Internet Explorer 8
* Firefox 3
* Adobe Flash Player 10

If you encounter any visual problems please upgrade your browser to the latest version in order to get the most out of our WIKI. Thank you!
Modelling - Overall Description
Personal note

I have never heard about the term ‘Synthetic Biology’ and the competition ‘iGEM’ until one day I received this email to recruit engineers. As I was hunting for something productive to do for the summer, and having had a strong interest in medicine and biology, I instantly applied for it. GREAT! Few days later, I joined the team, not knowing what the hell I was going to be working on.

Since then, I have learnt a lot more about biological systems, and ways to model them. Synthetic biology really is an AMAZING branch of research. The things you can design bacteria to do are limitless and will be never ending. iGEM has been a great way of self teaching, and motivation while working in a inter-disciplinary undergraduate team. I look forward to hearing about outstanding breakthroughs from ‘Synthetic Biology’ in the future.

WinHo
Our system requires a lot of components to function properly, so we decided the aim of our modelling would be to model different setups on how it should be put together, and pick the best one suited to the task of our biosensor. This is a cheap way of doing things, and can be done many times. This arrangement would then be made in the wet lab if time allowed.

We thought we would do something different this year from the traditional ordinary differential equations type modelling. The disadvantage of a model based on systems of differential equations is the necessity to enumerate every potential molecular species that could arise in the modelled system. Rule-based modelling on the other hand is much simpler. It describes biological interactions in terms of rules without the need to make presumptive choices about which terms to exclude from the model for simplification.

The modelling software we used is Cellucidate (Kappa language), an advanced, web-based platform for biological modelling. In Cellucidate, the molecular components of the cell are ‘agents’. These have sites that can undergo changes of state and can bind to the sites of other agents, as defined by the set of ‘rules’ that describe all of the permissible interactions between them. The dynamic behaviour of the modelled system can then be explored by executing the model using Cellucidate's stochastic simulator. The state of every agent in the system and every rule based events are observables, making the model easily understood. More details of this can be found here.

In addition to this, we also did some modelling of how the system would operate in real life which can be found here.

Edinburgh University iGEM Team 2009