Team:Grenoble/Modeling/Notebook/June

From 2012.igem.org

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<section>
<h1>June</h1>
<h1>June</h1>
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<a href="https://2012.igem.org/Team:Grenoble/Modeling/Notebook/June">Week 23</a> •  
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<a href="#23">Week 23</a> •  
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<a href="https://2012.igem.org/Team:Grenoble/Modeling/Notebook/June/week_24">Week 24</a> •  
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<a href="#24">Week 24</a> •  
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<a href="https://2012.igem.org/Team:Grenoble/Modeling/Notebook/June/week_25">Week 25</a> •  
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<a href="#25">Week 25</a> •  
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<a href="https://2012.igem.org/Team:Grenoble/Modeling/Notebook/June/week_26">Week 26</a>
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<a href="#26">Week 26</a>
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<section>
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<h1> Week 23: June 04<span class="exposant">th</span> to 10<span class="exposant">th</span> </h1>
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<h1 id="23"> Week 23: June 04<span class="exposant">th</span> to 10<span class="exposant">th</span> </h1>
 +
</br>
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<b> Goal </b>
 +
</br>
 +
<ul>
 +
<li>Beginning of the study of the ODE system on the AHL-LuxR circuit</li>
 +
<li>Sensitivity analysis on the AHL-LuxR circuit</li>
 +
</ul>
 +
</br>
 +
<b> Conclusion </b>
 +
</br>
 +
<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.
 +
</ul>
 +
</section>
 +
<section>
 +
<h1 id="24"> Week 24: June 11<span class="exposant">th</span> to 17<span class="exposant">th</span> </h1>
 +
</br>
 +
<b> Goal </b>
 +
</br>
 +
<ul>
 +
<li>Progress of ODEs on the AHL-LuxR circuit</li>
 +
<li>First complete modeling report about the AHL-LuxR circuit</li>
 +
<li>Stability analysis of the AHL-LuxR circuit</li>
 +
</ul>
 +
</br>
 +
<b> Conclusion </b>
 +
</br>
 +
<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.
 +
</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.
 +
</ul>
</section>
</section>
 +
 +
 +
<section>
 +
<h1 id="25"> Week 25: June 18<span class="exposant">th</span> to 24<span class="exposant">th</span> </h1>
 +
</br>
 +
<b> Goal </b>
 +
</br>
 +
<ul>
 +
<li>Design of the wiki</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>Research of parameters</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>
 +
</br>
 +
<b> Conclusion </b>
 +
</br>
 +
<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.
 +
</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.
 +
Finally, the article has been read and studied.
 +
</ul>
 +
</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> Conclusion </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>
 +
</div>
</div>

Latest revision as of 00:30, 25 September 2012

iGEM Grenoble 2012

iGEM Grenoble iGEM
iGEM 2012
main page
Project

June

Week 23 • Week 24 • Week 25 • Week 26

Week 23: June 04th to 10th


Goal
  • Beginning of the study of the ODE system on the AHL-LuxR circuit
  • Sensitivity analysis on the AHL-LuxR circuit

Conclusion
    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.

Week 24: June 11th to 17th


Goal
  • Progress of ODEs on the AHL-LuxR circuit
  • First complete modeling report about the AHL-LuxR circuit
  • Stability analysis of the AHL-LuxR circuit

Conclusion
    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.
    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.

Week 25: June 18th to 24th


Goal
  • Design of the wiki
  • Set a deterministic model with X,Y and Z in order to see if the circuit designed by the biologists could work
  • Research of parameters
  • Learn about Stochastic modeling and the Gillespie Algorithm (Reading of the article Stochastic Simulation of Chemical Kinetics from Daniel T. Gillespie)

Conclusion
    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 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. Finally, the article has been read and studied.

Week 26: June 25th to July 1st


Goal
  • Beginning of the study of the Quorum sensing
  • Redaction of the Grenoble part for the wiki

Conclusion
    To begin the study of the Quorum sensing, we made the resolution with ODE solver, but a lot of numerical instabilities.
    The presentation section of Grenoble is complete but needs to be checked by the advisors.

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