Team:Groningen/Brainstorm/Modelling

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Revision as of 10:46, 22 April 2009 by Jaspervdg (Talk | contribs)

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
  • 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 (?)
  • Genome Scale Model (whole cell response)
    • ETH Zurich 2008, using the [http://gcrg.ucsd.edu/Downloads/Cobra_Toolbox Cobra Toolbox] for Matlab
  • Chemostat simulation
  • Cell movement

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).