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 Artifitial Inteligence (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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Latest revision as of 15:22, 21 September 2011
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