Team:Southampton/Modeling

From 2009.igem.org

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iGEM 2009 Wiki</title>
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text-decoration:none;
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    <p>&nbsp;</p>
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    <p>&nbsp;</p>
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      <tr>
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</div>
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        <td><h3><span style="text-align: center">To
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<div id="H08_"> <img
+
          give the team some indication of the expected behaviour of our
-
id="H08" src="http://img190.imageshack.us/img190/6283/h08.jpg"
+
          completed systems, a simulation environment was made to allow the
-
alt="" height="45" width="138"> </div>
+
          models to interact with each other. More details of the simulation
-
<div id="I09_"> <a
+
          source code are to be released at a later date. The program is written
-
href="https://2009.igem.org/Team:Southampton/Sponsors"
+
          in Tcl [link http://wiki.tcl.tk/] and is designed to be easily modified
-
onmouseover="image7.src=loadImage7.src;"
+
          to model any system involving several cells interacting with each other
-
onmouseout="image7.src=staticImage7.src;"><img
+
          through the diffusion of chemical species.<br />
-
style="border: 0px solid ; width: 135px; height: 45px;" alt=""
+
          <br />
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name="image7"
+
          The results of an initial simulation of our Game of Life system are
-
src="http://img297.imageshack.us/img297/6668/i09.jpg"></a>
+
          presented below.<br />
-
</div>
+
          <br />
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<div id="J10_"> <img
+
          <img alt=""
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id="J10" src="http://img22.imageshack.us/img22/5245/j10osz.jpg"
+
  src="http://img211.imageshack.us/img211/6494/iptg.gif" /><br />
-
alt="" height="234" width="975"> </div>
+
          <br />
-
<div id="K11_"> <img
+
          The animation above shows an initial drop of IPTG being added to the
-
id="K11" src="http://img136.imageshack.us/img136/1714/baro.gif"
+
          system that activates the cells in its immediate vicinity. Note that
-
alt=""> </div>
+
          the IPTG does not diffuse throughout the system, not causing any
-
</div>
+
          effects other than the initial &lsquo;jump start&rsquo;.<br />
-
<div id="wrap">
+
          <br />
-
<div class="pagewrapper">
+
          <img alt=""
-
<div class="innerpagewrapper">
+
  src="http://img211.imageshack.us/img211/5158/luxi.gif" /><br />
-
<div class="page">
+
          <br />
-
<div class="content"><!-- CONTENT -->
+
          This animation shows the activated cells producing LuxI which then
-
<h3> </h3>
+
          diffuses to the rest of the system, activating further cells.<br />
-
<table style="text-align: left; width: 100%;"
+
          <br />
-
border="0" cellpadding="2" cellspacing="2">
+
          <img alt=""
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  <tbody>
+
  src="http://img376.imageshack.us/img376/6968/cells.gif" /><br />
-
    <tr>
+
          <br />
-
      <td>
+
          The final animation models the actual bacteria, randomly distributed
-
      <h3>&gt;&gt; Modelling</h3>
+
          throughout the system. Blue for those in the 'off' state and red for
-
      <p>Southampton University iGEM</p>
+
          those in the 'on' state.<br />
-
      </td>
+
          <br />
-
    </tr>
+
          An&nbsp; IPTG local density of 250 is required to switch a cell to
-
  </tbody>
+
          it's 'on' state. 'On' cells produce LuxI, turning on other cells when
-
</table>
+
          the local density of LuxI is greater than 50. When the local density of
-
<div style="text-align: center;">To
+
          LuxI is greater than 300, the cell switches to the 'off' state,
-
give the team some indication of the expected behaviour of our
+
          producing the characteristic ring. Note, all of the values above are
-
completed systems, a simulation environment was made to allow the
+
          arbitrary values and will be translated to molecule counts when
-
models to interact with each other. More details of the simulation
+
          empirical results are available.<br />
-
source code are to be released at a later date. The program is written
+
          <br />
-
in Tcl [link http://wiki.tcl.tk/] and is designed to be easily modified
+
          The figure below shows all three layers together, allowing easy
-
to model any system involving several cells interacting with each other
+
          comparison. To view the animations again, refresh this page.<br />
-
through the diffusion of chemical species.<br>
+
          <br />
-
<br>
+
          <img style="width: 400px; height: 107px;"
-
The results of an initial simulation of our Game of Life system are
+
-
presented below.<br>
+
-
<br>
+
-
<img alt=""
+
-
  src="http://img211.imageshack.us/img211/6494/iptg.gif"><br>
+
-
<br>
+
-
The animation above shows an initial drop of IPTG being added to the
+
-
system that activates the cells in its immediate vicinity. Note that
+
-
the IPTG does not diffuse throughout the system, not causing any
+
-
effects other than the initial &lsquo;jump start&rsquo;.<br>
+
-
<br>
+
-
<img alt=""
+
-
  src="http://img211.imageshack.us/img211/5158/luxi.gif"><br>
+
-
<br>
+
-
This animation shows the activated cells producing LuxI which then
+
-
diffuses to the rest of the system, activating further cells.<br>
+
-
<br>
+
-
<img alt=""
+
-
  src="http://img376.imageshack.us/img376/6968/cells.gif"><br>
+
-
<br>
+
-
The final animation models the actual bacteria, randomly distributed
+
-
throughout the system. Blue for those in the 'off' state and red for
+
-
those in the 'on' state.<br>
+
-
<br>
+
-
An&nbsp; IPTG local density of 250 is required to switch a cell to
+
-
it's 'on' state. 'On' cells produce LuxI, turning on other cells when
+
-
the local density of LuxI is greater than 50. When the local density of
+
-
LuxI is greater than 300, the cell switches to the 'off' state,
+
-
producing the characteristic ring. Note, all of the values above are
+
-
arbitrary values and will be translated to molecule counts when
+
-
empirical results are available.<br>
+
-
<br>
+
-
The figure below shows all three layers together, allowing easy
+
-
comparison. To view the animations again, refresh this page.<br>
+
-
<br>
+
-
<img style="width: 400px; height: 107px;"
+
  alt=""
  alt=""
-
  src="http://img35.imageshack.us/img35/2626/cellsiptgluxi400x.gif"><br>
+
  src="http://img35.imageshack.us/img35/2626/cellsiptgluxi400x.gif" /></span><br />
-
<br>
+
        </h3></td>
 +
      </tr>
 +
    </table>
 +
    <p>&nbsp;</p>
 +
    <p><br>
 +
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Revision as of 10:04, 15 September 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

Gallery

 

 

To give the team some indication of the expected behaviour of our completed systems, a simulation environment was made to allow the models to interact with each other. More details of the simulation source code are to be released at a later date. The program is written in Tcl [link http://wiki.tcl.tk/] and is designed to be easily modified to model any system involving several cells interacting with each other through the diffusion of chemical species.

The results of an initial simulation of our Game of Life system are presented below.



The animation above shows an initial drop of IPTG being added to the system that activates the cells in its immediate vicinity. Note that the IPTG does not diffuse throughout the system, not causing any effects other than the initial ‘jump start’.



This animation shows the activated cells producing LuxI which then diffuses to the rest of the system, activating further cells.



The final animation models the actual bacteria, randomly distributed throughout the system. Blue for those in the 'off' state and red for those in the 'on' state.

An  IPTG local density of 250 is required to switch a cell to it's 'on' state. 'On' cells produce LuxI, turning on other cells when the local density of LuxI is greater than 50. When the local density of LuxI is greater than 300, the cell switches to the 'off' state, producing the characteristic ring. Note, all of the values above are arbitrary values and will be translated to molecule counts when empirical results are available.

The figure below shows all three layers together, allowing easy comparison. To view the animations again, refresh this page.

 


Home | Project | Biobrick Parts | Team | Modelling | Notebook | Sponsors             University of Southampton iGEM 2009

Retrieved from "http://2009.igem.org/Team:Southampton/Modeling"