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Team:Groningen/Brainstorm/Modelling
From 2009.igem.org
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**[https://2008.igem.org/Team:UNIPV-Pavia/Modeling Pavia 2008], using Matlab and Simulink | **[https://2008.igem.org/Team:UNIPV-Pavia/Modeling Pavia 2008], using Matlab and Simulink | ||
**[https://2008.igem.org/Team:University_of_Ottawa/Modeling Ottawa 2008], using Matlab | **[https://2008.igem.org/Team:University_of_Ottawa/Modeling Ottawa 2008], using Matlab | ||
| + | **[https://2008.igem.org/Team:University_of_Washington/Modeling Washington 2008], using Mathematica | ||
| + | **[https://2008.igem.org/PHA_Project_Modeling Tsinghua 2008], using Matlab | ||
*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) | ||
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*Genome Scale Model (whole cell response) | *Genome Scale Model (whole cell response) | ||
**[https://2008.igem.org/Team:ETH_Zurich/Modeling/Genome-Scale_Model ETH Zurich 2008], using the [http://gcrg.ucsd.edu/Downloads/Cobra_Toolbox Cobra Toolbox] for Matlab | **[https://2008.igem.org/Team:ETH_Zurich/Modeling/Genome-Scale_Model ETH Zurich 2008], using the [http://gcrg.ucsd.edu/Downloads/Cobra_Toolbox Cobra Toolbox] for Matlab | ||
| + | **?[https://2008.igem.org/Team:Wisconsin/Modeling Wisconsin 2008], using GAMS | ||
*Chemostat simulation | *Chemostat simulation | ||
**[https://2008.igem.org/Team:ETH_Zurich/Modeling/Chemostat_Selection ETH Zurich 2008], using their genome scale model data | **[https://2008.igem.org/Team:ETH_Zurich/Modeling/Chemostat_Selection ETH Zurich 2008], using their genome scale model data | ||
*Cell movement | *Cell movement | ||
**[https://2008.igem.org/Team:iHKU/modeling IHKU 2008], as random walks | **[https://2008.igem.org/Team:iHKU/modeling IHKU 2008], as random walks | ||
| - | **[https://2008.igem.org/Team:University_of_Lethbridge/Modeling | + | **[https://2008.igem.org/Team:University_of_Lethbridge/Modeling Lethbridge 2008], using [http://www.pdn.cam.ac.uk/groups/comp-cell/BCT.html BCT] (a tool to model the chemotaxis pathway of E. Coli?) |
| + | **[https://2008.igem.org/Chemotaxis_Modeling Tsinghua 2008], using their own code? | ||
Other potentially interesting software tools: | Other potentially interesting software tools: | ||
Revision as of 10:59, 22 April 2009
Software tools from previous years
- RNA folding (secondary structure)
- Alberta 2008, using [http://rna.urmc.rochester.edu/rnastructure.html 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, [http://www.sbtoolbox2.org/main.php Systems Biology Toolbox 2] (sensitivity analysis) and [http://www.cellware.org/index.html CellWare] (stochastic analysis)
- Purdue 2008, using Excel and Mathcad
- TU Delft 2008, using CellDesigner and the [http://www.sys-bio.org/ Synthetic Biology Workbench] for Matlab
- Edinburgh 2008, using [http://www.copasi.org/tiki-index.php COPASI]
- Freiburg 2008, using Matlab
- Johns Hopkins 2008, using Matlab (for population dynamics of yeast)
- Michigan 2008, using Mathematica
- Pavia 2008, using Matlab and Simulink
- Ottawa 2008, using Matlab
- Washington 2008, using Mathematica
- Tsinghua 2008, using Matlab
- Cell processes
- Calgary 2008, using their own tool (transcription and translation)
- Waterloo 2008, using [http://theileria.ccb.sickkids.ca/CellSim/overview.php Cell++]
- Static genome analysis (?)
- ETH Zurich 2008, using their own tool
- Genome Scale Model (whole cell response)
- ETH Zurich 2008, using the [http://gcrg.ucsd.edu/Downloads/Cobra_Toolbox Cobra Toolbox] for Matlab
- ?Wisconsin 2008, using GAMS
- Chemostat simulation
- ETH Zurich 2008, using their genome scale model data
- Cell movement
- IHKU 2008, as random walks
- Lethbridge 2008, using [http://www.pdn.cam.ac.uk/groups/comp-cell/BCT.html BCT] (a tool to model the chemotaxis pathway of E. Coli?)
- Tsinghua 2008, using their own code?
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 [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).
