Team:Grenoble/Modeling/Notebook/September

From 2012.igem.org

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<a href="#36">Week 36</a> •  
<a href="#36">Week 36</a> •  
<a href="#37">Week 37</a> •  
<a href="#37">Week 37</a> •  
-
<a href="#38">Week 38</a> •  
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<a href="#38">Week 38</a> <!--•  
-
<a href="#39">Week 39</a>
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<a href="#39">Week 39</a> -->
</section>
</section>
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<section>
<section>
-
<h1 id="23"> Week 23: June 04<span class="exposant">th</span> to 10<span class="exposant">th</span> </h1>
+
<h1 id="36"> Week 36: September 03<span class="exposant">rd</span> to 09<span class="exposant">th</span> </h1>
</br>
</br>
<b> Goal </b>
<b> Goal </b>
</br>
</br>
<ul>
<ul>
-
<li>Beginning of the study of the ODE system on the AHL-LuxR circuit</li>
+
<li>new study with the stochastic modeling : adaptation of the scripts</li>
-
<li>Sensitivity analysis on the AHL-LuxR circuit</li>
+
<li>Continuation of the redaction for the stochastic part</li>
 +
<li>A final check for the receptor parameters</li>
 +
<li>Pooling the modeling parts</li>
</ul>
</ul>
</br>
</br>
-
<b> Completion </b>
+
<b> Conclusion </b>
</br>
</br>
<ul>
<ul>
-
We have begun to set the differential equations and the sensitivity analysis is done. This analysis was useful because we didn't really know the parameters and we needed to be sure that, even if they changed the behavior, the circuit would remain the same.
+
Regarding the stochastic modeling, the first part of the script has been modified and we are working on its optimization. The redaction progresses slowly.
-
</ul>
+
</br>
 +
Once the receptor’s parameters checked, we had to pool the signaling and the amplification models. We could thus estimate the sensitivity as well as the rapidity of our system. </ul>
</section>
</section>
<section>
<section>
-
<h1 id="24"> Week 24: June 11<span class="exposant">th</span> to 17<span class="exposant">th</span> </h1>
+
<h1 id="37"> Week 37: September 10<span class="exposant">th</span> to 16<span class="exposant">th</span> </h1>
</br>
</br>
<b> Goal </b>
<b> Goal </b>
</br>
</br>
<ul>
<ul>
-
<li>Progress of ODEs on the AHL-LuxR circuit</li>
+
<li>End of the stochastic changes</li>
-
<li>First complete modeling report about the AHL-LuxR circuit</li>
+
<li>Prepare our midi-minatec talk</li>
-
<li>Stability analysis of the AHL-LuxR circuit</li>
+
</ul>
</ul>
</br>
</br>
-
<b> Completion </b>
+
<b> Conclusion </b>
</br>
</br>
<ul>
<ul>
-
The ODEs are not already set but the report is done. The stability analysis lead to the fact that the system is locally stable. We could not tell if it's globally stable or not.
+
Unfortunately, because of a presentation to prepare, we didn't find time to end that stochastic modeling.
</br>
</br>
-
Nevertheless, after this week we stopped working on the AHL-LuxR circuit. This circuit is indeed an oscillator whereas we finally decided to design a detector.
+
The modeling team worked hard during this week to choose which results were worth presenting and which not. Then we thought with the biologists of a clear and simple way of presenting our work and making synthetic biology accessible even for uninitiated. You can visit the section Human practice- promoting synthetic biology to know more about this event.  
</ul>
</ul>
</section>
</section>
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<section>
<section>
-
<h1 id="25"> Week 25: June 18<span class="exposant">th</span> to 24<span class="exposant">th</span> </h1>
+
<h1 id="38"> Week 38: September 17<span class="exposant">th</span> to 23<span class="exposant">rd</span> </h1>
</br>
</br>
<b> Goal </b>
<b> Goal </b>
</br>
</br>
<ul>
<ul>
-
<li>Design of the wiki</li>
+
<li>End of the stochastic modeling and analyse of the results</li>
-
<li>Set a deterministic model with X,Y and Z in order to see if the circuit designed by the biologists could work</li>
+
<li>End of the redaction for the stochastic part</li>
-
<li>Research of parameters</li>
+
<li>Prepare the modeling section and put our main results on line</li>
-
<li>Learn about Stochastic modeling and the Gillespie Algorithm (Reading of the article <u>Stochastic Simulation of Chemical Kinetics</u> from Daniel T. Gillespie)</li>
+
</ul>
</ul>
</br>
</br>
-
<b> Completion </b>
+
<b> Conclusion </b>
</br>
</br>
<ul>
<ul>
-
A first essay of a possible design for the wiki has been made. The ODEs for the deterministic system are set but they depend on parameters. The graphs of that model seem to meet our expectations.
+
The stochastic modeling is definitely finished and the whole stochastic part in the wiki is written with analyses on the results.
</br>
</br>
-
The research of some parameters has been made in the previous iGEM’s wikis (degradation rate of arabinose & transcription/translation rate of araC found on team PKU beijing 2009’s wiki). Otherwise, a first stochastic model of the new circuit including cya & the enzymatic reaction has been set. The output is actually amplified but not as much as required. We are wondering if the inefficiency is due to a modeling problem or the structure of the biological system.
+
Most parts of the modeling section are ready and put online. As for us, we tried to make it as clear as possible. Hope you’ll enjoy it.
-
Finally, the article has been read and studied.
+
</ul>
</ul>
</section>
</section>
-
<section>
 
-
<h1 id="26"> Week 26: June 25<span class="exposant">th</span> to July 1<span class="exposant">st</span> </h1>
 
-
</br>
 
-
<b> Goal </b>
 
-
</br>
 
-
<ul>
 
-
<li>Beginning of the study of the Quorum sensing</li>
 
-
<li>Redaction of the Grenoble part for the wiki</li>
 
-
</ul>
 
-
</br>
 
-
<b> Completion </b>
 
-
</br>
 
-
<ul>
 
-
To begin the study of the Quorum sensing, we made the resolution with ODE solver, but a lot of numerical instabilities.
 
-
</br>
 
-
The presentation section of Grenoble is complete but needs to be checked by the advisors.
 
-
</ul>
 
-
</section>
 

Latest revision as of 03:01, 27 September 2012

iGEM Grenoble 2012

iGEM Grenoble iGEM
iGEM 2012
main page
Project

September

Week 36 • Week 37 • Week 38

Week 36: September 03rd to 09th


Goal
  • new study with the stochastic modeling : adaptation of the scripts
  • Continuation of the redaction for the stochastic part
  • A final check for the receptor parameters
  • Pooling the modeling parts

Conclusion
    Regarding the stochastic modeling, the first part of the script has been modified and we are working on its optimization. The redaction progresses slowly.
    Once the receptor’s parameters checked, we had to pool the signaling and the amplification models. We could thus estimate the sensitivity as well as the rapidity of our system.

Week 37: September 10th to 16th


Goal
  • End of the stochastic changes
  • Prepare our midi-minatec talk

Conclusion
    Unfortunately, because of a presentation to prepare, we didn't find time to end that stochastic modeling.
    The modeling team worked hard during this week to choose which results were worth presenting and which not. Then we thought with the biologists of a clear and simple way of presenting our work and making synthetic biology accessible even for uninitiated. You can visit the section Human practice- promoting synthetic biology to know more about this event.

Week 38: September 17th to 23rd


Goal
  • End of the stochastic modeling and analyse of the results
  • End of the redaction for the stochastic part
  • Prepare the modeling section and put our main results on line

Conclusion
    The stochastic modeling is definitely finished and the whole stochastic part in the wiki is written with analyses on the results.
    Most parts of the modeling section are ready and put online. As for us, we tried to make it as clear as possible. Hope you’ll enjoy it.

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