# Team:Groningen/Brainstorm/Modelling

### From 2009.igem.org

## 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?

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).