Team:Groningen/Brainstorm/Modelling

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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
  • 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)
  • Chemostat simulation
  • 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?
  • 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
    • Conways game of life
    • Ecolicence to kill: Engineering E.coli for targeting pathogenic microorganisms
    • Dr. Coli, the bacterial drug delivery system
    • 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
    • Light sensing
    • 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 [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).