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Team:Groningen/Brainstorm/Modelling
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Revision as of 20:01, 27 April 2009
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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)
- Michigan 2008, using Mathematica
- Pavia 2008, using Matlab and Simulink
- Ottawa 2008, using Matlab
- Washington 2008, using Mathematica
- Tsinghua 2008, using Matlab
- BCCS-Bristol 2008, Matlab
- Groningen 2008!, using Matlab and some custom tools to construct the models
- KULeuven, using Matlab and Celldesigner, site done very decently
- Montreal, using Mathematica
- Paris 2008, using BIOCHAM
- UCSF, using Matlab, Klaas Bernd: perhaps for growth stages?
- Cambridge, using an unspecified tool
- Imperial College Londen, using Matlab
- Peking, using Symbiology
- Cell processes
- Calgary 2008, using their own tool (transcription and translation)
- Waterloo 2008, using Cell++
- 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
- ?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 BCT (a tool to model the chemotaxis pathway of E. Coli?)
- Tsinghua 2008, using their own code?
- Group behaviour
- BCCS-Bristol 2008, movement of groups of cells, using a home-grown Java tool
- Groningen 2008!, spatial interaction
- Heidelberg, two population distributions and some substance concentrations using custom Matlab code
- Montreal, interaction in Repressilator network, using Mathematica
- Cambridge, quorum sensing
- Imperial College Londen, growth curve and motility, using Matlab
- Mutation
Other potentially interesting software tools:
- UC Berkeley's Clotho
- SBML? (language to specify models)
- KU Leuven's Simbiology2LaTeX
