Team:Southampton/Modeling

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<h1>Modelling</h1>
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<h1>Project Achievements</h1>
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      <td bgcolor="#5D5D5D"><h4 align="center">&nbsp;</h4>
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            <td width="520" valign="top" bgcolor="#5D5D5D"><ul>
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                <h3>We have submitted documentation for 20    registry parts for our two subprojects &ndash; <a href="https://2009.igem.org/Team:Southampton/Parts/GoL">Game of Life</a> and <a href="https://2009.igem.org/Team:Southampton/Parts/RPS">Rock-paper-scissors</a>.</h3>
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              <h3>&nbsp;</h3></td>
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                <h3>A new biobrick part of our own construction, <a href="http://partsregistry.org/Part:BBa_K180000">Ptac</a>, has been sequenced,    submitted and documented on the registry. </h3>
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              </li>
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              <h3>&nbsp;</h3></td>
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                <h3>The <a href="https://2009.igem.org/Team:Southampton/Project/Safety">safety    considerations</a> of our project were thoroughly investigated with the    completion of two GMO (genetically modified organism) forms and accompanying    risk assessments. </h3>
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              <h3>&nbsp;</h3></td>
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                <h3>We have participated in an ethics    questionnaire for the Valencia team and have received a Valencia gold medal    for 100% team participation.</h3>
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              <h3><img src="https://static.igem.org/mediawiki/2009/8/82/Clip_image002_0003.jpg" alt=":::V_Southampton.JPG" width="76" height="76" hspace="12" border="1" align="right" /></h3>
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              <h3>&nbsp;</h3></td>
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            <td valign="top" bgcolor="#5D5D5D">&nbsp;</td>
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                <h3><a href="https://2009.igem.org/Team:Southampton/Modeling">Modelling</a> of our cell networks for both the Game of Life and Rock Paper Scissors subprojects. </h3>
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              </li>
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                <h3>A <a href="https://2009.igem.org/Team:Southampton/Modeling/Open">simulation program</a> has been produced that can be used to model any bacterial diffusion system    and this has been made accessible to anyone.</h3>
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              <h3>&nbsp;</h3></td>
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                <h3>We have left an <a href="https://2009.igem.org/Team:Southampton/HP/Legacy">outreach legacy</a>,    which has become integrated into the School of Chemistry outreach programme    at the University of Southampton.</h3>
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              <h3>&nbsp;</h3></td>
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                <h3>A video, showing our <a href="https://2009.igem.org/Team:Southampton/HP/igemexper">iGEM2009 experience</a>,    has been produced and is freely available online for all to view.</h3>
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              <h3>&nbsp;</h3></td>
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                <h3>Awareness has been raised in the field of    synthetic biology through the <a href="https://2009.igem.org/Team:Southampton/HP/Outreach">outreach project</a> with secondary school students (age 11-16), and through <a href="https://2009.igem.org/Team:Southampton/HP/Political">interviews</a> and    a <a href="https://2009.igem.org/Team:Southampton/HP/Legacy">synthetic biology    briefing</a> with MPs (Ministers of Parliament) in our constituencies. </h3>
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              <p>&nbsp;</p></td>
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<h3>&nbsp;</h3>
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        <td bgcolor="#5D5D5D"><h3>In modelling our cell networks, we found it helpful to  visualize our machines at a higher level of abstraction than the ubiquitous  plasmid map. Flow charts were chosen to efficiently represent the dynamics of  the system, borrowing from the engineering concept of finite state-machines.</h3>
 
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          <h3>In our Game of Life system, there is only one &lsquo;machine&rsquo; type  and two diffusing molecules, IPTG and LuxI. As this is slightly simpler than  Rock-Paper-Scissors, with its three machine types and molecules, we implemented  the Game of Life model first.</h3>
 
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          <h3>A simulator was designed to interpret the flow charts and  model the system to produce spatio-temporal patterns. The simulation  environment is defined by an adjustable square grid, typically 100 x 100 for  our simulations. The environment is divided into several layers, starting with  the cell layer. Each location on the grid can be occupied by a single cell of a  predefined type and state. As the simulation progresses cells can change state  in response to the diffusion of molecules in the layers below them, as defined  by their state transition rules. Below the cell layer reside the molecule  layers, with each molecule occupying its own layer. Each grid location holds a  number representing the total number of molecules present in that space. A  diffusion algorithm runs constantly during simulations, allowing a high  concentration of molecules in one area to diffuse to an area of lower  concentration. As each molecule resides on its own layer they never interact  with each other.          </h3>
 
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          <h3>The simulator is written in <a href="http://wiki.tcl.tk/">Tcl</a>            and relies heavily on the <a href="http://tcl-nap.sourceforge.net/">NAP</a>&nbsp;extension for fast array  processing. Simulation durations are defined by the number of times the  diffusion algorithm is run and it typically requires about 2 x 10^5 iterations  for an initial drop of a molecule in the centre of the grid to diffuse to the  edges (for a 100 x 100 grid). On the ageing laboratory P4 it took about 90  minutes to run the simulation described above.</h3>
 
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          <h3>After generating several interesting results from the Game  of Life simulation, we looked to modifying the system to simulate our  Rock-Paper-Scissors models. Much of the source code was the same for both  systems leading us to wonder, &lsquo;What if there was a program that could simulate  any system with mechanisms similar to ours?&rsquo; The simulator was generalized to  allow it to be used with any system involving the production and diffusion of  chemical products between cellular machines. A user interface was also added to  allow non-programmers to enter their models and run simulations of their own.</h3>
 
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          <h3>The results of our simulations can be at the <a href="https://2009.igem.org/Team:Southampton/Modeling/GoL">Game of  Life</a>&nbsp;and <a href="https://2009.igem.org/Team:Southampton/Modeling/RPS">Rock-Paper-Scissors</a> pages.</h3>
 
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          <h3>The simulator package is available for download from the <a href="https://2009.igem.org/Team:Southampton/Modeling/Open">Open  Access</a>&nbsp;page. Although it  currently has all of the features required to model our systems and those  similar to them, there is much more that can be done. The program has been  open-sourced and instructions on how to acquire the source can also be found there.</h3>
 
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<h5>| <a href="#">Top</a> |&nbsp; &nbsp;&nbsp;&nbsp;
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Revision as of 20:08, 21 October 2009

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> University of Southampton Wiki

Project Achievements

.

 

 

  • A new biobrick part of our own construction, Ptac, has been sequenced, submitted and documented on the registry.

 

  • The safety considerations of our project were thoroughly investigated with the completion of two GMO (genetically modified organism) forms and accompanying risk assessments.

 

  • We have participated in an ethics questionnaire for the Valencia team and have received a Valencia gold medal for 100% team participation.

:::V_Southampton.JPG

 

 
  • Modelling of our cell networks for both the Game of Life and Rock Paper Scissors subprojects.

  • A simulation program has been produced that can be used to model any bacterial diffusion system and this has been made accessible to anyone.

 

  • We have left an outreach legacy, which has become integrated into the School of Chemistry outreach programme at the University of Southampton.

 

  • A video, showing our iGEM2009 experience, has been produced and is freely available online for all to view.

 

 

 

 

 

 

 

 

 

C
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