Team:Grenoble/Projet/Design

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    <h1>Modelling</h1>
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  <h2>Table of content</h2>  
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<h1>Genetic Network</h1>
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  Our synthetic biology constructions feature tens of parameters and at this scale human brains can only guess how the whole system would work. We of course needed mathematical modelling in order to check the effectiveness of the genetic circuit.<br/><br/>
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<p>
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we design the following circuit, based on Gardner and al. Gardner's <a href="#1">[1]</a> work and balagadd and al. on Predator–Prey ecosystem <a href="#2">[2]</a>.
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<center><a href="https://static.igem.org/mediawiki/2011/8/80/Reseau_regulation_compl2_%281%29.png"><img height="400" src="https://static.igem.org/mediawiki/2011/8/80/Reseau_regulation_compl2_%281%29.png"></a></center>
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<p>
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It can be divided into four parts: the Toggle Switch, the Quorum Sensing, the Coloration and the post-transcriptional regulation. (Coloration is included in Quorum Sensing page) </p>
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  In the particular case of our circuit and final use of the bacteria, the modelling team also had to give the specificities (size, number of bacteria, IPTG gradient specificities) of the measuring device we intend to produce.<br/><br/>
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        <div class="blocbackground">
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<h2>Table of content</h2>
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  In the next pages we expose which algorithms we used for both deterministic modelling and stochastic modelling, explain our MATLAB scripts (available <a href="http://igemgrenoble-files.perso.sfr.fr/2011/MATLAB_Archives/">here</a>) and finally give the results of our simulations.<br/><br/>
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  <a href="https://2011.igem.org/Team:Grenoble/Projet/Modelling/Deterministic" ><img class="icon" src="https://static.igem.org/mediawiki/2011/b/b4/Icon_deterministic.png"/></a>
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      <big><big><a href="https://2011.igem.org/Team:Grenoble/Projet/Modelling/Deterministic" class="menu">Deterministic Modelling :</a></big></big><br/>
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<a class="menu">Our equations and how we obtained them.</a><br/>
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<a class="menu">Our algorithms</a><br/>
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<a class="menu">Isoclines and Hysteresis</a><br/><br/>
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  <a ><img class="icon" src="https://static.igem.org/mediawiki/2011/6/67/Icon_stochastic.png"/></a>
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<big><big><a class="menu">Stochastic Modelling :</a></big></big><br/>
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<a class="menu">Geoffrey</a><br/>
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<a class="menu">Gillespie algorithm</a><br/>
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<a class="menu">Mean, standard deviation and statistical properties</a><br/><br/>
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  <a><img class="icon" src="https://static.igem.org/mediawiki/2011/3/34/Icon_parameters.png"/></a>
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<br/><big><big><a class="menu">Parameters</a></big></big><br/><br/><br/><br/>
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  <a><img class="icon" src="https://static.igem.org/mediawiki/2011/e/e1/Icon_results.png"/></a>
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In the following pages, you can find the explanation about the differents sub-parts of our genetic network. Moreover we explane to you the importance of both to our project.
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      <big><big><a class="menu">Results :</a></big></big><br/>
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      <a class="menu">Validation of our genetical network</a><br/>
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      <a class="menu">Device</a><br/><br/>
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    </p>
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For an introduction to the genetic circuit, see our tutorials in the human practice
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section or download them here :
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<ul>
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<li>
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<a href="https://static.igem.org/mediawiki/2011/9/91/M_for_B.png">
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Modelling for biologist</a>
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</li>
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<li>
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<a href="https://static.igem.org/mediawiki/2011/5/54/B_for_M.png">
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Synthetic Biology for modellers</a>
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</li>
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</ul>
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<br/><br/>
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<a href="https://2011.igem.org/Team:Grenoble/Projet/Design/toggle"><img class="icon" src="https://static.igem.org/mediawiki/2011/2/20/Bouton_toggle.png"/></a>
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<big><big><a href="https://2011.igem.org/Team:Grenoble/Projet/Design/toggle" class="menu">Toggle Switch:</a></big></big><br/>
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<a href="https://2011.igem.org/Team:Grenoble/Projet/Design/quorum" class="menu"><img class="icon" src="https://static.igem.org/mediawiki/2011/f/f8/Bouton_QS_color.png"/></a>
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<big><big><a href="https://2011.igem.org/Team:Grenoble/Projet/Design/quorum" class="menu">Quorum Sensing :</a></big></big><br/>
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<a  href="https://2011.igem.org/Team:Grenoble/Projet/Design/quorum" class="menu">The Quorum Sensing</a><br/>
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<a  href="https://2011.igem.org/Team:Grenoble/Projet/Design/quorum#coloration" class="menu">Coloration</a><br/>
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<a href="https://2011.igem.org/Team:Grenoble/Projet/regulation" ><img class="icon" src="https://static.igem.org/mediawiki/2011/9/97/Bouton_regulation.png"/></a>
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<big><big><a href="https://2011.igem.org/Team:Grenoble/Projet/regulation" class="menu">Post-transcriptional regulation :</a></big></big><br/>
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<a  href="https://2011.igem.org/Team:Grenoble/Projet/regulation" class="menu">A post-transcriptional regulation system</a><br/>
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<a  href="https://2011.igem.org/Team:Grenoble/Projet/regulation#rsma" class="menu">The RsmA translational regulation system</a><br/>
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<a  href="https://2011.igem.org/Team:Grenoble/Projet/regulation#rpos" class="menu">The rpoS regulation system</a><br/>
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<br/><br/><br/>
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</p>
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<p>
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You can find the results of our biological experiments in the
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<a href="https://2011.igem.org/Team:Grenoble/Projet/Results">results page
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</a>.
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        </p>
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<h2>References :</h2>
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<li id="1">
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GARDNER'S WORK: "Construction of a genetic toggle switch in Escherichia coli", Timothy S. Gardner, Charles R. Cantor and James J. Collins, Nature, 2000, Vol.403, p339-42.
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</li>
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<li id="2">
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PREY AND PREDATOR: "A synthetic Escherichia coli predator–prey ecosystem", Frederick K Balagadd, Hao Song, Jun Ozaki, Cynthia H Collins, Matthew Barnet, Frances H Arnold, Stephen R Quake and Lingchong You, Molecular Systems Biology, 2008;4:187.
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                                     <option value="/Deterministic#Our_equations" >Our equations</option>
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                                     <option value="/Design/toggle" >The Toggle Switch</option>
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                                     <option value="/Design/quorum">The Quorum Sensing</option>
                                  
                                  
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                                     <option value="/Design/quorum#coloration">The Coloration</option>
                                  
                                  
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                                    <option value="/Stochastic#Stats">Mean, standard deviation and stats</option>
 
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    <option value="/regulation">A Post-Transcriptional Regulation System</option>
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Latest revision as of 18:24, 31 January 2012

Grenoble 2011, Mercuro-Coli iGEM


Genetic Network

we design the following circuit, based on Gardner and al. Gardner's [1] work and balagadd and al. on Predator–Prey ecosystem [2].



It can be divided into four parts: the Toggle Switch, the Quorum Sensing, the Coloration and the post-transcriptional regulation. (Coloration is included in Quorum Sensing page)



Table of content

In the following pages, you can find the explanation about the differents sub-parts of our genetic network. Moreover we explane to you the importance of both to our project.

For an introduction to the genetic circuit, see our tutorials in the human practice section or download them here :

Toggle Switch:




Quorum Sensing :
The Quorum Sensing
Coloration


Post-transcriptional regulation :
A post-transcriptional regulation system
The RsmA translational regulation system
The rpoS regulation system



You can find the results of our biological experiments in the results page .

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iGEM 2011 Main Page


Contact Us:

Clic here !

Retrieved from "http://2011.igem.org/Team:Grenoble/Projet/Design"