|
|
| (8 intermediate revisions not shown) |
| Line 1: |
Line 1: |
| - | 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.
| |
| - | * 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.
| |
| - | * 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]]
| |
| - |
| |
| - | ==Modeling blog==
| |
| - | 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.
| |
| - |
| |
| - |
| |
| - | {| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
| |
| - | !align="center"|[[Team:Groningen|Home]]
| |
| - | !align="center"|[[Team:Groningen/Team|Team]]
| |
| - | !align="center"|[https://igem.org/Team.cgi?year=2010&team_name=Groningen Official Team Profile]
| |
| - | !align="center"|[[Team:Groningen/Project|Project]]
| |
| - | !align="center"|[[Team:Groningen/Parts|Parts Submitted to the Registry]]
| |
| - | !align="center"|[[Team:Groningen/Modeling|Modeling]]
| |
| - | !align="center"|[[Team:Groningen/Notebook|Notebook]]
| |
| - | !align="center"|[[Team:Groningen/Safety|Safety]]
| |
| - | !align="center"|[[Team:Groningen/Attributions|Attributions]]
| |
| - | |}
| |
"
