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T4: Logical modelling of regulatory networks - BC^2

Tutorial: Logical modelling of regulatory networks, June 9th


    Instructors
  • Claudine Chaouiya (IGC, Oeiras PT)
  • Isaac Crespo (Vital-IT, SIB Lausanne CH)
  • Julien Dorier (Vital-IT, SIB Lausanne CH)
  • Pedro Monteiro (INESC, Lisbon PT)
  • AurĂ©lien Naldi (UM2, Montpellier FR)
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Schedule (&: slides): Please note, starting time at 13:45!

13:45-14:15Introduction to logical modelling (SLIDES)
14:15-14:45Software tools, and overview, SBML & CoLoMoTo (SLIDES)
14:45-15:15Logical models of T helper cells activation and differentiation (SLIDES)
15:15-15:30The Cell Collective - Short demo
15:30-16:00Coffee Break
16:00-16:50SQUAD, BoolSim - Demo & hands on (Presentation slidesSQUAD tutorialSLIDES boolSim)
16:50-17:40GINsim, Model checking - Demo & hands on (SLIDES GINsimSLIDES Model-checking)

Compressed folder with all the slides.

Instructions for hands-on sessions

To avoid compatibility problems between different operating systems and potentially missing libraries, we opted to provide all the necessary material in the form of a Virtual Machine containing all the programs, models and scripts for the hands-on session.

Virtual Machine Installation

  1. VirtualBox platform installation
    Download the VirtualBox platform package for your specific Operating System (Windows, Linux, OS X, ...) at https://www.virtualbox.org/wiki/Downloads
  2. Install the BC2-Tutorial-T4 virtual machine
    1. Download the virtual machine at https://ulisboa-my.sharepoint.com/personal/ist146963_tecnico_ulisboa_pt/_layouts/15/guestaccess.aspx?guestaccesstoken=sgh0OMx1YFrSWGfngzyRlRLT3g160uEJfIenlN6mGwY%3d&docid=002d134d2e85f4c3494fc282468b77f36
      (you'll need 3.1Gb available - can take approximately 1 hour!)
    2. Open VirtualBox, select File -> Import Appliance and choose the downloaded file BC2-Tutorial-T4.ova
      This will uncompress the virtual machine to be used by VirtualBox (you'll additionally need 7.7Gb available)
    3. The imported machine should appear on the left of your VirtualBox window. Select it and press Start to launch it.
    4. Login password is squad1234

Installation/Performance issues
Contact us by email at or on site at the BC2 conference before the Tutorial.

References

  1. Th models
  2. Squad & boolSim
  3. GINsim
    • D. Bérenguier, C. Chaouiya, P. T. Monteiro, A. Naldi, E. Remy, D. Thieffry, and L. Tichit, "Dynamical modeling and analysis of large cellular regulatory networks", Chaos 23, 025114 (2013) URL: http://dx.doi.org/10.1063/1.4809783
  4. The Cell Collective
    • Helikar T, Kowal B, McClenathan S, Bruckner M, Rowley T, Madrahimov A, Wicks B, Shrestha M, Limbu K, Rogers JA. "The Cell Collective: toward an open and collaborative approach to systems biology", BMC Syst Biol. 6:96 (2012) URL: http://www.biomedcentral.com/1752-0509/6/96

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