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Team:CIDEB-UANL Mexico/Math/Overview
From 2012hs.igem.org
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| + | <a name="Acknowledgements"></a>Acknowledgements | ||
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| + | <center><b><p><i>I want to thank to my advisors for the Math Model Daniel Gerardo Rodriguez Reyna and Heber Torres Cordero, for the time they gave to me and to this project. And also I want to thank to my father Rubén Navarro Reyes and my mother Liliana Castillo Ramirez for giving me the facilities to be in this team and also my father to help me with any doubt I had about anything related to the project and life. I don’t know how to pay all the effort that the people I mentioned has done. But I hope this little effort that I did not comparable with theirs can be a demonstration of what they’ve created through me. | ||
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| + | <right><p><i><b>Ruben Navarro Castillo</b></i></p></right> | ||
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| + | <a name="MathModel"></a>Math Model | ||
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| + | <p><i>Math model Team: Rubén Navarro Castillo</i></p> | ||
| + | <p>We’ve decided to use a deterministic math model for our circuit because we considered that this is more appropriate for this circuit.</p> | ||
| + | <p>We’ve been using the traditional differential equations for the description of the production of proteins and mRNA that are described here: <b>d[xmRNA]/dt = k1*f(yreg)-γ1 [xmRNA] y d[xprotein]/dt = k2*[xmRNA]-γ2 [xprotein] ]-f(post) *[xprotein].</b></p> | ||
| + | <p>To get the maximum transcription and maximum translation rates we used the ecuations recommended by <a href="https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters" title="Beijing 2009">iGEM Beijing 2009 </a>that are:</p> | ||
| + | <p>Maximum Transcription Rate = Transcription Speed(nt/min)/Gene Length(bp)</p> | ||
| + | <p>Translation Rate = RBS * Translation Speed(Aa/min)/Protein Length(Aa)</p> | ||
| + | <p>As our circuit is inside a E. Coli we’ve decided to use the speed of transcription and traduction as: 70 nt/s y 40Aa/s respectively.</p> | ||
| + | <p>For the description of the binding of araC and arabinose in order to switch on the promoter pBAD, we’ve followed the recommendations of <a href=" https://2009.igem.org/Team:Cambridge/Modelling" title="Cambridge 2009">Cambridge 2009</a>: as a way of repressing the promoter pBAD and it is showed in the section of differential equations.</p> | ||
| + | <p>You can find out the entire system described with differential equations in the page of equations and the parameters in the page of parameters.</p> | ||
| + | <p><b>References:</b><p> | ||
| + | <li><a href="https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters">https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters</a> | ||
| + | <li><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters" title="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters">https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Parameters</a></li> | ||
| + | <li><a href="https://2010.igem.org/Team:Brown/Modeling/ODEs" title="https://2010.igem.org/Team:Brown/Modeling/ODEs>https://2010.igem.org/Team:Brown/Modeling/ODEs</a></li> | ||
| + | <li><a href="https://2009.igem.org/Team:Cambridge/Modelling" title="https://2009.igem.org/Team:Cambridge/Modelling">https://2009.igem.org/Team:Cambridge/Modelling</a></li> | ||
| + | <li><a href="https://2011.igem.org/Team:St_Andrews/modelling" title="https://2011.igem.org/Team:St_Andrews/modelling">https://2011.igem.org/Team:St_Andrews/modelling</a></li> | ||
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Latest revision as of 03:59, 22 July 2012
I want to thank to my advisors for the Math Model Daniel Gerardo Rodriguez Reyna and Heber Torres Cordero, for the time they gave to me and to this project. And also I want to thank to my father Rubén Navarro Reyes and my mother Liliana Castillo Ramirez for giving me the facilities to be in this team and also my father to help me with any doubt I had about anything related to the project and life. I don’t know how to pay all the effort that the people I mentioned has done. But I hope this little effort that I did not comparable with theirs can be a demonstration of what they’ve created through me.
Ruben Navarro Castillo
Math model Team: Rubén Navarro Castillo
We’ve decided to use a deterministic math model for our circuit because we considered that this is more appropriate for this circuit.
We’ve been using the traditional differential equations for the description of the production of proteins and mRNA that are described here: d[xmRNA]/dt = k1*f(yreg)-γ1 [xmRNA] y d[xprotein]/dt = k2*[xmRNA]-γ2 [xprotein] ]-f(post) *[xprotein].
To get the maximum transcription and maximum translation rates we used the ecuations recommended by iGEM Beijing 2009 that are:
Maximum Transcription Rate = Transcription Speed(nt/min)/Gene Length(bp)
Translation Rate = RBS * Translation Speed(Aa/min)/Protein Length(Aa)
As our circuit is inside a E. Coli we’ve decided to use the speed of transcription and traduction as: 70 nt/s y 40Aa/s respectively.
For the description of the binding of araC and arabinose in order to switch on the promoter pBAD, we’ve followed the recommendations of Cambridge 2009: as a way of repressing the promoter pBAD and it is showed in the section of differential equations.
You can find out the entire system described with differential equations in the page of equations and the parameters in the page of parameters.
References:
