Team:Groningen/Modeling

From 2011.igem.org

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Because of the device-like nature of out project modeling plays a big part. This page gives an overview of some of our organistional considerations and provides links to the more practical aspects. A big consideration is that our modeling team comes from the local AI department and has significant experience in modeling in matlab.
 
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==Methods==
 
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First of all we have to decide in what enviorment we want to model in. There is a lot of different software out there. Our 2009 team did a large survey on modeling packages used in Igem [https://2009.igem.org/Team:Groningen/Brainstorm/Modelling]. Our whitebook also included several biomodeling packages that we should look at:
 
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*[[Team:Groningen/Modeling/SynBioSS|SynBioSS]]
 
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*[[Team:Groningen/Modeling/CellDesigner|CellDesigner]]
 
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*[[Team:Groningen/Modeling/COPASI|COPASI]]
 
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*[[Team:Groningen/Modeling/Matlab with SimBiology|Matlab with SimBiology]]
 
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Although COPASI and SimBiology seemed really nice (be sure to look at it when in doubt) we decided to go with matlab for the following reasons:
 
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* Freedom of programming: Although the matlab programming syntax is rather cumborsome (espcially when using OOP) we are sure it can produce anything we want.
 
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* Popularety: There is a very large userbase for matlab and plenty of support for it. Many other iGEM teams use it so it will be easy to share our finings and models.
 
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* Great plotting and visalisation option: this will allow us to see what is going on without the hassle of exporting and importing the data to other packages.
 
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* Familiarety of the team: Not having to learn using a program from the beginning is a big advantage. Some of our members have years of experience with matlab and have no problem implementing anything in matlab.
 
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==Library==
 
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We are currently developing our own modeling library and hopefully we will be able to finish it in time for other teams to use it. It will be geared towards beginning/intermediate matlab users who want to model single cell processes.
 
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==Modules==
 
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We decided to build our model in the samen modules as the cloners will use. Because of the fragilety of the by stable switches these should be modeled first.
 
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*[[Team:Groningen/Modeling/Module 1|Module 1]]
 
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==Modeling blog==
 
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You can check our modeling progress on our [[Team:Groningen/Modeling/Modeling Blog|modeling blog]]. This will contain weekly updates of our progress and some highligths of our results.
 
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
 
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!align="center"|[[Team:Groningen|Home]]
 
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!align="center"|[[Team:Groningen/Team|Team]]
 
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!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=Groningen Official Team Profile]
 
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!align="center"|[[Team:Groningen/Project|Project]]
 
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!align="center"|[[Team:Groningen/Parts|Parts Submitted to the Registry]]
 
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!align="center"|[[Team:Groningen/Modeling|Modeling]]
 
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!align="center"|[[Team:Groningen/Notebook|Notebook]]
 
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!align="center"|[[Team:Groningen/Safety|Safety]]
 
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!align="center"|[[Team:Groningen/Attributions|Attributions]]
 
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|}
 

Latest revision as of 15:22, 21 September 2011