Team:Southampton/Modeling

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">   University of Southampton Wiki    /*TOOLBAR*/ position:absolute; left:-2px; top:0px; width:978px; height:27px; z-index:100; } /*FOOTERPUSH*/ width:1px; height:1633px; } html, body { margin: 0; padding: 0; } /*LAYOUT BEGINS*/ width: 80%; left: 20% } position:absolute; left:0px; top:296px; width:975px; height:1410px; background-image:url('http://www.personal.soton.ac.uk/jeh2v07/images/bg.gif'); background-repeat:repeat-y; margin: 0; padding: 0; }	position:absolute; left:113px; top:1675px; z-index:150; color: #333; }	position:absolute; left:0px; top:1645px; width:975px; height:61px; z-index:100; }    Home  Project <![if gt IE 6]><![endif]>  <li class=" cssMenui">Project Aims</a></li> <li class=" cssMenui">Project Introduction</a></li> <li class=" cssMenui">Project Description</a></li> <li class=" cssMenui">Project Achievements</a></li> <li class=" cssMenui">Project Projection</a></li> <li class=" cssMenui">Project Safety</a></li> <li class=" cssMenui">References and Links</a></li> <li class=" cssMenui"> Protocols <![if gt IE 6]></a><![endif]> <ul class=" cssMenum"> <li class=" cssMenui">Protocol Overview</a></li> <li class=" cssMenui">Protocol Theory</a></li> <li class=" cssMenui">Biobrick Transformation</a></li> <li class=" cssMenui">Colony PCR</a></li> <li class=" cssMenui">DNA Double Digestion</a></li> <li class=" cssMenui">Gel Electrophoresis</a></li> <li class=" cssMenui">High Fidelity PCR</a></li> <li class=" cssMenui">LB Plates</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Project/Protocols/Ligation">Ligation</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Project/Protocols/Ligationtransformation">Ligation Transformation</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Project/Protocols/PlasmidPrep">Plasmid Preparation</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Project/Protocols/TA">TA Cloning</a></li> </ul> </li> </ul> </li> <li class=" cssMenui"><a class=" cssMenui" href="#">Biobrick Parts<![if gt IE 6]></a><![endif]> <ul class=" cssMenum"> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Parts/GoL">Game of Life</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Parts/RPS">Rock Paper Scissors</a></li> </ul></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Team"> Team <![if gt IE 6]></a><![endif]> <ul class=" cssMenum"> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Team">Team Profiles</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Team/Advisors">Advisor Profiles</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Team/Southampton">Southampton Profile</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Team/University">University Profile</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Team/Gallery">Gallery</a></li> </ul> </li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Modeling"> Modelling <![if gt IE 6]></a><![endif]> <ul class=" cssMenum"> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Modeling">Modelling Overview</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Modeling/GoL">Game Of Life</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Modeling/RPS">Rock Paper Scissors</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Modeling/Open">Open Access</a></li> </ul> </li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/HP"> Human Practices <![if gt IE 6]></a><![endif]> <ul class=" cssMenum"> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/HP">Overview</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/HP/Outreach">Outreach</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/HP/igemexper">iGEM Experience</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/HP/Political">Political Awareness</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/HP/Legacy">Our Legacy</a></li> </ul> </li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Notebook">Notebook</a><![endif]> <ul class=" cssMenum">
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<li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Notebook">Notebook</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Notebook/Labbook">Lab Book</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Notebook/Advisorblog">Advisor Blog</a></li> </ul> </li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Sponsors"> Acknowledgments <![if gt IE 6]></a><![endif]> <ul class=" cssMenum"> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Sponsors">Sponsors</a></li> <li class=" cssMenui"><a class=" cssMenui" href="http://2009.igem.org/Team:Southampton/Southampton">Team Southampton</a></li> </ul> </li> </ul> <img style="width: 975px; height: 24px;" id="bg" src="http://www.personal.soton.ac.uk/jeh2v07/images/maintop.gif" alt="" /> <img style="width: 63px; height: 63px;" alt="" src="http://www.personal.soton.ac.uk/jeh2v07/images/logobox.jpg" /> Modelling 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> 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. 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. The results of our simulations can be at the <a href="http://2009.igem.org/Team:Southampton/Modeling/GoL">Game of Life</a> and <a href="http://2009.igem.org/Team:Southampton/Modeling/RPS">Rock-Paper-Scissors</a> pages. The simulator package is available for download from the <a href="http://2009.igem.org/Team:Southampton/Modeling/Open">Open Access</a> 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.

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