Team:Groningen/Brainstorm/Modelling

From 2009.igem.org

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m (Interactive Graphs?: Link to spreadsheet)
m (Software tools from previous years: Symbiology -> SimBiology)
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*Molecular/genetic Circuit (?), (small) systems of (non-linear) ODEs
*Molecular/genetic Circuit (?), (small) systems of (non-linear) ODEs
**[https://2008.igem.org/Team:Bologna/Modeling Bologna 2008], using Simulink (Mathworks)
**[https://2008.igem.org/Team:Bologna/Modeling Bologna 2008], using Simulink (Mathworks)
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**[https://2008.igem.org/Team:ETH_Zurich/Modeling/Switch_Circuit ETH Zurich 2008], using the Symbiology toolbox in Matlab
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**[https://2008.igem.org/Team:ETH_Zurich/Modeling/Switch_Circuit ETH Zurich 2008], using the SimBiology toolbox in Matlab
**[https://2008.igem.org/Team:iHKU/modeling IHKU 2008]
**[https://2008.igem.org/Team:iHKU/modeling IHKU 2008]
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**(?)[https://2008.igem.org/Team:Istanbul/Modeling Istanbul 2008], using the Symbiology toolbox
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**(?)[https://2008.igem.org/Team:Istanbul/Modeling Istanbul 2008], using the SimBiology toolbox
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**[https://2008.igem.org/Team:LCG-UNAM-Mexico/Modeling LCG-UNAM-Mexico 2008], using the Symbiology toolbox
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**[https://2008.igem.org/Team:LCG-UNAM-Mexico/Modeling LCG-UNAM-Mexico 2008], using the SimBiology toolbox
**[https://2008.igem.org/Team:NTU-Singapore/Modelling/Deterministic_Modeling NTU Singapore 2008], using Simulink, [http://www.sbtoolbox2.org/main.php Systems Biology Toolbox 2] (sensitivity analysis) and [http://www.cellware.org/index.html CellWare] (stochastic analysis)
**[https://2008.igem.org/Team:NTU-Singapore/Modelling/Deterministic_Modeling NTU Singapore 2008], using Simulink, [http://www.sbtoolbox2.org/main.php Systems Biology Toolbox 2] (sensitivity analysis) and [http://www.cellware.org/index.html CellWare] (stochastic analysis)
**[https://2008.igem.org/Team:Purdue/Modeling Purdue 2008], using Excel and Mathcad
**[https://2008.igem.org/Team:Purdue/Modeling Purdue 2008], using Excel and Mathcad
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**[https://2008.igem.org/Team:Cambridge/Modelling Cambridge], using an unspecified tool
**[https://2008.igem.org/Team:Cambridge/Modelling Cambridge], using an unspecified tool
**[https://2008.igem.org/Team:Imperial_College/Dry_Lab Imperial College Londen], using Matlab
**[https://2008.igem.org/Team:Imperial_College/Dry_Lab Imperial College Londen], using Matlab
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**[https://2008.igem.org/Team:Peking_University/Modeling Peking], using Symbiology
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**[https://2008.igem.org/Team:Peking_University/Modeling Peking], using SimBiology
*Cell processes
*Cell processes
**[https://2008.igem.org/Modeling Calgary 2008], using their own tool (transcription and translation)
**[https://2008.igem.org/Modeling Calgary 2008], using their own tool (transcription and translation)

Revision as of 15:33, 28 April 2009

[http://2009.igem.org/Team:Groningen http://2009.igem.org/wiki/images/f/f1/Igemhomelogo.png]


Software tools from previous years

Other potentially interesting software tools:

Interactive Graphs?

It might be interesting to use JavaScript to present simulation results. This would allow for some degree of interaction (like resizing graphs, linked views, etc.) and may even make it somewhat easier to use graphs, we'd simply have some on-line repository of simulation results (a spreadsheet for example) and we could select which graphs to use on the Wiki.

Below an example of a JavaScript generated graph is shown, based on [http://spreadsheets.google.com/pub?key=rRnyFyi-bgqsjT3SdJBdKKw this spreadsheet]. Note that the two views of the data are linked (although at this time both the kind of graph and the link is not optimal) and that it would be possible to create templates for creating these linked graphs. The current demo is based on Google technology, but it looks like [http://www.dojotoolkit.org/ the Dojo Toolkit] has more advanced charting capabilities at this moment (although I don't know how well they're supported in different browsers).

Taking this idea (much) further it would even be possible to run simulations using JavaScript (and charting the results), based on SBML models. However, this would involve much, much more effort than just showing a few interactive plots.

Literature

See our literature list. For our team members that are looking for books on the subject, have a look under code [http://opc.ub.rug.nl/DB=1/SET=2/TTL=1/CLK?IKT=8110&TRM=605B 605B] (Bernoulliborg library, lower floor), as well as 605C/D/E (A and Z also exist but seem to be less interesting) and 610A (and possibly 625, 715).