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Team:Groningen/Brainstorm/Modelling
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| + | !align="center"|[[Team:Groningen|Home]] | ||
| + | !align="center"|[[Team:Groningen/Team|The Team]] | ||
| + | !align="center"|[[Team:Groningen/Brainstorm|Brainstorm]] | ||
| + | !align="center"|[[Team:Groningen/Vision|Our Vision]] | ||
| + | !align="center"|[[Team:Groningen/Parts|Parts]] | ||
| + | !align="center"|[[Team:Groningen/Modelling|Modelling]] | ||
| + | !align="center"|[[Team:Groningen/Notebook|Notebook]] | ||
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==Software tools from previous years== | ==Software tools from previous years== | ||
Revision as of 08:26, 23 April 2009
| Home | The Team | Brainstorm | Our Vision | Parts | Modelling | Notebook |
|---|
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
- 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?
- NEED TO MERGE
- Gene Regulatory Networks (GRNs)
- Stochastic Agent Based Simulation
- Hybrid Model (BSim v2)
- Genetic Network Generating Spatial Patterns Through Cell-Cell Communication and Controlled Information Processing
- EPF-Lausanne, need to find exactly what they did.
- Conways game of life
- Groningen!, singel cell
- Groningen, spatial approach
- Groningen, modeling files
- Ecolicence to kill: Engineering E.coli for targeting pathogenic microorganisms
- Dr. Coli, the bacterial drug delivery system
- KULeuven, done very decently
- Occilations in large numbers of cells
- Montreal, done in mathematica, serveral years of research
- Bacterial Clock
- Paris, see how this fits in one of our projects
- Cellular Memory
- UCSF, perhaps for growth stages?
- Quorum sensing
- Cambridge, Perhaps for growth stages?
- Light sensing
- Imperial College Londen, mayby for one of our projects.
- The floating Bacteria
- Kyoto, lets have a very good look at what these guys have been doing
- Genetic Cricuit
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), as well as 605C/D/E (A and Z also exist but seem to be less interesting).
