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Team:Groningen/Brainstorm/Modelling
From 2009.igem.org
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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
- 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 [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?
- 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
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) and 610A (and possibly 625, 715).
