Team:Groningen/Brainstorm/Modelling
From 2009.igem.org
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**[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 | ||
**[https://2008.igem.org/Team:TUDelft/Color_modeling TU Delft 2008], using CellDesigner and the [http://www.sys-bio.org/ Synthetic Biology Workbench] for Matlab | **[https://2008.igem.org/Team:TUDelft/Color_modeling TU Delft 2008], using CellDesigner and the [http://www.sys-bio.org/ Synthetic Biology Workbench] for Matlab | ||
+ | **[https://2008.igem.org/Team:Edinburgh/Modelling/Kinetic Edinburgh 2008], using [http://www.copasi.org/tiki-index.php COPASI] | ||
+ | **[https://2008.igem.org/Team:Freiburg/Modeling Freiburg 2008], using Matlab | ||
+ | **[https://2008.igem.org/Team:Johns_Hopkins/Applications Johns Hopkins 2008], using Matlab (for population dynamics of yeast) | ||
*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 10:29, 22 April 2009
Software tools from previous years
- RNA folding (secondary structure)
- Alberta 2008, using RNAstructure and UNAFold (with a front-end), they used both programs (presumably to get an idea of the certainty)
- Molecular/genetic Circuit (?), (small) systems of (non-linear) ODEs
- Bologna 2008, using Simulink (Mathworks)
- ETH Zurich 2008, using the Symbiology toolbox in Matlab
- IHKU 2008
- (?)Istanbul 2008, using the Symbiology toolbox
- LCG-UNAM-Mexico 2008, using the Symbiology toolbox
- NTU Singapore 2008, using Simulink, Systems Biology Toolbox 2 (sensitivity analysis) and CellWare (stochastic analysis)
- Purdue 2008, using Excel and Mathcad
- TU Delft 2008, using CellDesigner and the Synthetic Biology Workbench for Matlab
- Edinburgh 2008, using COPASI
- Freiburg 2008, using Matlab
- Johns Hopkins 2008, using Matlab (for population dynamics of yeast)
- Cell processes
- Calgary 2008, using their own tool (transcription and translation)
- Static genome analysis (?)
- ETH Zurich 2008, using their own tool
- Genome Scale Model (whole cell response)
- ETH Zurich 2008, using the Cobra Toolbox for Matlab
- Chemostat simulation
- ETH Zurich 2008, using their genome scale model data
- Cell movement
- IHKU 2008, as random walks
- University of Lethbridge 2008, using BCT (a tool to model the chemotaxis pathway of E. Coli?)
Other potentially interesting software tools:
Literature
See our literature list. For our team members that are looking for books on the subject, have a look under code 605B (Bernoulliborg library, lower floor).