Team:Groningen/Modeling

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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|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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~~Alothough COPASI 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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* Popularaty: 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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~~==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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-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.
-==Methods==
-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|whitebook]] also included several biomodeling packages that we should look at:
-*[[Team:Groningen/Modeling/SynBioSS|SynBioSS]]
-*[[Team:Groningen/Modeling/CellDesigner|CellDesigner]]
-*[[Team:Groningen/Modeling/COPASI|COPASI]]
-*[[Team:Groningen/Modeling/Matlab with SimBiology|Matlab with SimBiology]]
-Alothough COPASI seemed really nice (be sure to look at it when in doubt) we decided to go with matlab for the following reasons:
-* Freedom of programming: Although the matlab programming syntax is rather cumborsome (espcially when using OOP) we are sure it can produce anything we want.
-* Popularaty: 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.
-* 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.
-* 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.
-==Modules==
-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.
-*[[Team:Groningen/Modeling/Module 1|Module 1]]

From 2011.igem.org

Latest revision as of 15:22, 21 September 2011