Team:Grenoble/Modeling/Notebook/August/31

From 2012.igem.org

(Difference between revisions)
(Blanked the page)
 
Line 1: Line 1:
-
{{:Team:Grenoble/Templates/Modeling}}
 
-
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
 
-
<body id="Modeling">
 
-
<div id="cadre">
 
-
<section>
 
-
<h1>August</h1>
 
-
<a href="http://2012.igem.org/Team:Grenoble/Modeling/Notebook/August#1">Week 31</a> •
 
-
<a href="http://2012.igem.org/Team:Grenoble/Modeling/Notebook/August#2">Week 32</a> •
 
-
<a href="http://2012.igem.org/Team:Grenoble/Modeling/Notebook/August#3">Week 33</a> •
 
-
<a href="http://2012.igem.org/Team:Grenoble/Modeling/Notebook/August#4">Week 34</a> •
 
-
<a href="http://2012.igem.org/Team:Grenoble/Modeling/Notebook/August#5">Week 35</a>
 
-
</section>
 
-
 
-
<br/>
 
-
 
-
<section>
 
-
<h1 id="1"> Week 31: July 30<span class="exposant">th</span> to August 5<span class="exposant">th</span> </h1>
 
-
</br>
 
-
<b> Goal </b>
 
-
</br>
 
-
<ul>
 
-
<li>Know if there is a basal production of Cya</li>
 
-
<li>Determine modeling for the receptor</li>
 
-
</ul>
 
-
</br>
 
-
<b> Completion </b>
 
-
</br>
 
-
<ul>
 
-
There is no wild type in the experiments, but thanks to the glucose we can say that there is no basal production of Gfp/Cya (it is the same because they are regulated by the same promotor.
 
-
The problem with the receptor model is that we have a lot of equations and thus too much parameters (16). After a meeting with our advisors we decided to simplify the equations and chose a different model.
 
-
</br>
 
-
For the deterministic model of the receptor, we chose to model reactions of the receptor behavior by a series of complexations. We got the inspiration from iGEM Imperial College 2010.
 
-
The graphs obtained weren't satisfying so we decided to review the parameters values.
 
-
</ul>
 
-
</section>
 
-
 
-
<section>
 
-
<h1 id="2"> Week 32: August 6<span class="exposant">th</span> to 12<span class="exposant">th</span> </h1>
 
-
</br>
 
-
<b> Goal </b>
 
-
</br>
 
-
<ul>
 
-
<li>Parameters research for the receptor model</li>
 
-
<li>Script and simulation for the stochastic model</li>
 
-
<li>Comparaison between the systems with the amplification loop and without. However without the loop we don't consider the degradation.</li>
 
-
</ul>
 
-
</br>
 
-
<b> Completion </b>
 
-
</br>
 
-
<ul>
 
-
The script for the stochastic model and its optimisation is done but there are problems because of parameters.
 
-
</br>
 
-
We can have a better result with the amplificationn loop if we amplify CRP. However we face a new problem : the system could be always turned on.
 
-
</ul>
 
-
</section>
 
-
 
-
<section>
 
-
<h1 id="3"> Week 33: August 13<span class="exposant">th</span> to 19<span class="exposant">th</span> </h1>
 
-
</br>
 
-
<b> Goal </b>
 
-
</br>
 
-
<ul>
 
-
<li>End of the script for the stochastic and analysis</li>
 
-
<li>Beginning of the equilibrium analysis to answer the question : Is the system always turned on ?</li>
 
-
<li>Set a new deterministic model for the receptor</li>
 
-
</ul>
 
-
</br>
 
-
<b> Completion </b>
 
-
</br>
 
-
<ul>
 
-
The script is definitely done but the parameters are not fixed. Thus we can't make simulations and analyse the results.
 
-
</br>
 
-
We learnt how to use isoclines.
 
-
</br>
 
-
For the receptor we chose a phenomenological extension of Goldbeter-Koshland biochemical switch model[1]. </br>The system is now much simple. We have 2 equations and 8 parameters.</br></br></br>
 
-
[1] Alejandra C.Ventura, Jacques-A. Sepulchre, Sofia D.Merajver. A Hidden Feedback in Signaling Cascades Is Revealed. PLOS Computational Biology, 2008, 4, 3, e1000041.
 
-
</ul>
 
-
</section>
 
-
 
-
<section>
 
-
<h1 id="4"> Week 34: August 20<span class="exposant">th</span> to 26<span class="exposant">th</span> </h1>
 
-
</br>
 
-
<b> Goal </b>
 
-
</br>
 
-
<ul>
 
-
<li>End of the stochastic</li>
 
-
<li>Redaction of the stochastic part</li>
 
-
<li>Equilibrium analysis</li>
 
-
<li>Determine which parameters we should modify to get better results</li>
 
-
</ul>
 
-
</br>
 
-
<b> Completion </b>
 
-
</br>
 
-
For the stochastic part we are still waiting on parameters. Concerning the redaction of the stochastic part, we can't progress seeing that we can't analyse our results yet.
 
-
</br>
 
-
It seems that we reach the wanted equilibriums only if the basal production of Ca is zero. We modified the ODE to make them be always right.
 
-
</section>
 
-
 
-
<section>
 
-
<h1 id="5"> Week 35: August 27<span class="exposant">th</span> to September 02<span class="exposant">nd</span> </h1>
 
-
</br>
 
-
<b> Goal </b>
 
-
</br>
 
-
<ul>
 
-
<li>Check the receptor modell</li>
 
-
<li>End of stochastic and redaction for the wiki</li>
 
-
<li>Equilibrium analysis on a simplified model to compute the threshold under which the equilibrium point changes</li>
 
-
</ul>
 
-
</br>
 
-
<b> Completion </b>
 
-
</br>
 
-
<ul>
 
-
The receptor model and the stochastic model are checked. All the equilibrium analysis are done. We should work with more CRP and a little arabinose. For the receptor script we have a problem with the curve of AC evolution : it decreases at high dipeptide concentration.We're thinking about the origin of the problem.
 
-
</ul>
 
-
</section>
 
-
 
-
</div>
 
-
</body>
 
-
</html>
 
-
{{:Team:Grenoble/script}}
 
-
{{:Team:Grenoble/menu}}
 

Latest revision as of 00:16, 25 September 2012