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Team:Southampton/Modeling
From 2009.igem.org
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| - | + | <h3>>> Modelling</h3> | |
| - | + | <p>Southampton University iGEM</p> | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | <h3>>> | + | |
| - | <p>Southampton University | + | |
</td> | </td> | ||
</tr> | </tr> | ||
</tbody> | </tbody> | ||
</table> | </table> | ||
| + | <div style="text-align: center;">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.<br> | ||
| + | <br> | ||
| + | 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 ‘jump start’.<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 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="" | ||
| + | src="http://img35.imageshack.us/img35/2626/cellsiptgluxi400x.gif"><br> | ||
| + | <br> | ||
| + | </div> | ||
| + | |||
<!-- END CONTENT --> </div> | <!-- END CONTENT --> </div> | ||
<div class="sidebar"><!-- SIDEBAR --> | <div class="sidebar"><!-- SIDEBAR --> | ||
Revision as of 15:53, 27 August 2009
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
>> ModellingSouthampton University iGEM |
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.
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.
