Team:Grenoble/Modeling/Notebook/August/31

From 2012.igem.org

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</ul>
</section>
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<h1> Week 32: August 6<span class="exposant">th</span> to 12<span class="exposant">th</span> </h1>
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</br>
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<b> Goal </b>
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</br>
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<ul>
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<li>Parameters research for the receptor model</li>
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<li>Script and simulation for the stochastic model</li>
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<li>Comparaison between the systems with the amplification loop and without. However without the loop we don't consider the degradation.</li>
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</ul>
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</br>
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<b> Completion </b>
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</br>
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<ul>
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The script for the stochastic model and its optimisation is done but there are problems because of parameters.
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</br>
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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.
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</ul>
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</section>
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<section>
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<h1> Week 33: August 13<span class="exposant">th</span> to 19<span class="exposant">th</span> </h1>
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</br>
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<b> Goal </b>
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</br>
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<ul>
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<li>End of the script for the stochastic and analysis</li>
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<li>Beginning of the equilibrium analysis to answer the question : Is the system always turned on ?</li>
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<li>Set a new deterministic model for the receptor</li>
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</ul>
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</br>
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<b> Completion </b>
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</br>
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<ul>
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The script is definitely done but the parameters are not fixed. Thus we can't make simulations and analyse the results.
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</br>
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We learnt how to use isoclines.
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</br>
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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>
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[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.
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</ul>
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</section>
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<section>
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<h1> Week 34: August 20<span class="exposant">th</span> to 26<span class="exposant">th</span> </h1>
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</br>
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<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.
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</section>
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 +
 +
</div>
</div>
</body>
</body>

Revision as of 00:14, 25 September 2012

iGEM Grenoble 2012

iGEM Grenoble iGEM
iGEM 2012
main page
Project

August

Week 31 • Week 32 • Week 33 • Week 34 • Week 35

Week 31: July 30th to August 5th


Goal
  • Know if there is a basal production of Cya
  • Determine modeling for the receptor

Completion
    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.
    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.

Week 32: August 6th to 12th


Goal
  • Parameters research for the receptor model
  • Script and simulation for the stochastic model
  • Comparaison between the systems with the amplification loop and without. However without the loop we don't consider the degradation.

Completion
    The script for the stochastic model and its optimisation is done but there are problems because of parameters.
    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.

Week 33: August 13th to 19th


Goal
  • End of the script for the stochastic and analysis
  • Beginning of the equilibrium analysis to answer the question : Is the system always turned on ?
  • Set a new deterministic model for the receptor

Completion
    The script is definitely done but the parameters are not fixed. Thus we can't make simulations and analyse the results.
    We learnt how to use isoclines.
    For the receptor we chose a phenomenological extension of Goldbeter-Koshland biochemical switch model[1].
    The system is now much simple. We have 2 equations and 8 parameters.


    [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.

Week 34: August 20th to 26th


Goal
  • End of the stochastic
  • Redaction of the stochastic part
  • Equilibrium analysis
  • Determine which parameters we should modify to get better results

Completion
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.
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.

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