Team:Grenoble/Projet/Modelling

From 2011.igem.org

(Difference between revisions)
Line 7: Line 7:
<html>
<html>
-
 
-
<img src="http://www.clickartists.org/clicksite/html/images/square.jpg"/>
 
<!--
<!--
 +
<img src="http://www.clickartists.org/clicksite/html/images/square.jpg"/>
 +
Si vous éditez la page commencez par décommenter ces lignes, publier, PUIS commencer à faire ce que vous avez à faire et quand vous avez fini de publier remettez en commentaire.
Si vous éditez la page commencez par décommenter ces lignes, publier, PUIS commencer à faire ce que vous avez à faire et quand vous avez fini de publier remettez en commentaire.
Line 44: Line 44:
since they evolve both in time and space. To help future teams with similar calculations, we explain
since they evolve both in time and space. To help future teams with similar calculations, we explain
in details the algorithms that were used and provide the scripts <a href="http://igemgrenoble-files.perso.sfr.fr/2011/MATLAB_Archives/">here</a>.
in details the algorithms that were used and provide the scripts <a href="http://igemgrenoble-files.perso.sfr.fr/2011/MATLAB_Archives/">here</a>.
-
The modelling results are described in the last section.
+
The modelling results are described in the last section.<br/><br/>
 +
 +
For an introduction to the modelling of biological genetic circuit see our tutorials in the human practice
 +
section or download them here :
 +
<ul>
 +
<li>
 +
<a href="https://static.igem.org/mediawiki/2011/9/91/M_for_B.png">
 +
Modelling for biologist</a>
 +
</li>
 +
<li>
 +
<a href="https://static.igem.org/mediawiki/2011/5/54/B_for_M.png">
 +
Synthetic Biology for modellers</a>
 +
</li>
 +
</ul>
 +
<br/><br/>
<br/><br/>
Line 58: Line 72:
<big><big><a class="menu" href="https://2011.igem.org/Team:Grenoble/Projet/Modelling/Stochastic">Stochastic Modelling :</a></big></big><br/>
<big><big><a class="menu" href="https://2011.igem.org/Team:Grenoble/Projet/Modelling/Stochastic">Stochastic Modelling :</a></big></big><br/>
       
       
-
<a class="menu" href="https://2011.igem.org/Team:Grenoble/Projet/Modelling/Stochastic#Geof">Sensitivity to noise</a><br/>
+
<a class="menu" href="https://2011.igem.org/Team:Grenoble/Projet/Modelling/Stochastic#Geof">Sensitivity to noise: a first approach</a><br/>
<a class="menu" href="https://2011.igem.org/Team:Grenoble/Projet/Modelling/Stochastic#Gillespie_algorithm">Gillespie algorithm</a><br/>
<a class="menu" href="https://2011.igem.org/Team:Grenoble/Projet/Modelling/Stochastic#Gillespie_algorithm">Gillespie algorithm</a><br/>
<a class="menu" href="https://2011.igem.org/Team:Grenoble/Projet/Modelling/Stochastic#Stats">Mean, standard deviation and statistical properties</a><br/><br/>
<a class="menu" href="https://2011.igem.org/Team:Grenoble/Projet/Modelling/Stochastic#Stats">Mean, standard deviation and statistical properties</a><br/><br/>
Line 71: Line 85:
     
     
    <p>
    <p>
-
You can find the results of our modelling results in the <a href="https://2011.igem.org/Team:Grenoble/Projet/Results">results page</a>.
+
You can find our modelling results <a href="https://2011.igem.org/Team:Grenoble/Projet/Results">here</a>.
    </p>
    </p>
Line 77: Line 91:
</div>
</div>
-
<div class="menu_deroulant_au_centre">
+
 
-
<form method="get" >
+
<form method="get" >
-
+
  <input type="button" value="< PREVIOUS <" onclick="document.location = '/Team:Grenoble/Projet/Modelling';" />
-
<input type="button" value="< PREVIOUS <" onclick="document.location = '/Team:Grenoble/Projet/Modelling';" />
+
  <select name="id" onchange="document.location = '/Team:Grenoble/Projet/Modelling' + this.options[this.selectedIndex].value ;">
-
+
 
-
<select name="id" onchange="document.location = '/Team:Grenoble/Projet/Modelling' + this.options[this.selectedIndex].value ;">
+
    <optgroup label="Modelling Homepage">
-
+
   
-
<optgroup label="Modelling Homepage">
+
    <option value="#Content" selected="selected">Table of content</option>
-
<option value="#Content" selected="selected">Table of content</option>
+
 
-
</optgroup>
+
    </optgroup>
-
+
 
-
<optgroup label="Construction of the model" >
+
    <optgroup label="Construction of the model" >
-
<option value="/Deterministic#Our_EquationsTS" >Establishment of the equation - Toggle switch</option>
+
                               
-
<option value="/Deterministic#Our_EquationsQS" >Establishment of the equation - Quorum sensing</option>
+
                                    <option value="/Deterministic#Our_EquationsTS" >Establishment of the equation - Toggle switch</option>
-
<option value="/Deterministic#Our_algorithms" >Our algorithms</option>
+
 
-
</optgroup>
+
                                    <option value="/Deterministic#Our_EquationsQS" >Establishment of the equation - Quorum sensing</option>
-
+
                               
-
<optgroup label="Stochastic Modelling">
+
                                    <option value="/Deterministic#Our_algorithms" >Our algorithms</option>
-
<option value="/Stochastic#Geof">Sensitivity to noise</option>
+
                               
-
<option value="/Stochastic#Gillespie_algorithm">Gillespie algorithm</option>
+
                                   
-
<option value="/Stochastic#Stats">Mean, standard deviation and stats</option>
+
                            </optgroup>
-
</optgroup>
+
                       
-
+
                            <optgroup label="Stochastic Modelling">
-
<optgroup label="Parameters">
+
                               
-
<option value="/Parameters">Table of parameters</option>
+
                                    <option value="/Stochastic#Geof">Sensitivity to noise</option>
-
<option value="/Parameters">Sensitivity to parameters</option>
+
                               
-
</optgroup>
+
                                    <option value="/Stochastic#Gillespie_algorithm">Gillespie algorithm</option>
-
+
                               
-
</select>
+
                                    <option value="/Stochastic#Stats">Mean, standard deviation and stats</option>
-
+
 
-
<input type="hidden" name="id2" value="0" />
+
                            </optgroup>
-
<input type="submit" value="Go!" />
+
 
-
<input type="button" value="> NEXT >" onclick="document.location = '/Team:Grenoble/Projet/Modelling/Deterministic';" />
+
                            <optgroup label="Parameters">
-
</form>
+
                           
-
</div>
+
    <option value="/Parameters">Table of parameters</option>
 +
    <option value="/Parameters">Sensitivity to parameters</option>
 +
 
 +
    </optgroup>
 +
                    </select>
 +
                    <input type="hidden" name="id2" value="0" />
 +
                    <input type="submit" value="Go!" />
 +
  <input type="button" value="> NEXT >" onclick="document.location = '/Team:Grenoble/Projet/Modelling/Deterministic';" />
 +
               
 +
            </form>
</div>
</div>
Line 122: Line 145:
</html>
</html>
-
{{:Team:Grenoble/Design/pied}}
 

Revision as of 16:26, 28 October 2011

Grenoble 2011, Mercuro-Coli iGEM


Modelling

The modelling team is responsible for:

  1. Verifying that the designed genetic circuit elicits the desired behavior in E coli. A deterministic model of the circuit has been developed in order to predict the dynamical behavior of the circuit in the presence of a concentration gradient of IPTG and various concentrations of Mercury or aTc (anhydrotetracycline).
  2. Providing specifications for the quantification device (size, number of bacteria, IPTG gradient). The apparition of the red line indicating the presence and quantity of Mercury or aTc is sensitive to fluctuations in the concentration of these molecules and IPTG. We took into account these fluctuations in a stochastic version of the circuit model, which we have used to determine the specifications of our device.

Table of content

In the following pages, we detail the development of the deterministic and stochastic models, together with their dynamical analysis. Solving numerically these systems required tricky calculations, since they evolve both in time and space. To help future teams with similar calculations, we explain in details the algorithms that were used and provide the scripts here. The modelling results are described in the last section.

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



Construction of the model :
Establishment of the equation Toggle switchQuorum sensing
Our algorithms


Stochastic Modelling :
Sensitivity to noise: a first approach
Gillespie algorithm
Mean, standard deviation and statistical properties

Parameters
Table of parameters
Sensitivity to parameters


You can find our modelling results here.

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