Team:Grenoble/Modeling/Notebook/June/25

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<h1>June</h1>
 
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<a href="http://2012.igem.org/Team:Grenoble/Modeling/Notebook/June/23">Week 23</a> •
 
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<a href="http://2012.igem.org/Team:Grenoble/Modeling/Notebook/June/24">Week 24</a> •
 
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<a href="http://2012.igem.org/Team:Grenoble/Modeling/Notebook/June/25">Week 25</a> •
 
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<a href="http://2012.igem.org/Team:Grenoble/Modeling/Notebook/June/26">Week 26</a>
 
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<h1> Week 25: June 18<span class="exposant">th</span> to 24<span class="exposant">th</span> </h1>
 
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<b> Goal </b>
 
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<ul>
 
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<li>Design of the wiki</li>
 
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<li>Set a deterministic model with X,Y and Z in order to see if the circuit designed by the biologists could work</li>
 
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<li>Research of parameters</li>
 
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<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>
 
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<b> Completion </b>
 
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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.
 
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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.
 
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Finally, the article has been read and studied.
 
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Latest revision as of 00:15, 25 September 2012