Tutorial: Logical modelling of regulatory networks, June 9th
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Schedule (&: slides): Please note, starting time at 13:45!
| 13:45-14:15 | Introduction to logical modelling (SLIDES) |
| 14:15-14:45 | Software tools, and overview, SBML & CoLoMoTo (SLIDES) |
| 14:45-15:15 | Logical models of T helper cells activation and differentiation (SLIDES) |
| 15:15-15:30 | The Cell Collective - Short demo |
| 15:30-16:00 | Coffee Break |
| 16:00-16:50 | SQUAD, BoolSim - Demo & hands on (Presentation slides, SQUAD tutorial, SLIDES boolSim) |
| 16:50-17:40 | GINsim, Model checking - Demo & hands on (SLIDES GINsim, SLIDES 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
- VirtualBox platform installation
Download the VirtualBox platform package for your specific Operating System (Windows, Linux, OS X, ...) at https://www.virtualbox.org/wiki/Downloads - Install the BC2-Tutorial-T4 virtual machine
- 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!) - 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) - The imported machine should appear on the left of your VirtualBox window. Select it and press Start to launch it.
- Login password is squad1234
Installation/Performance issues
Contact us by email at or on site at the BC2 conference before the Tutorial.
References
- Th models
- L. Mendoza & I. Xenarios, "A method for the generation of standardized qualitative dynamical systems of regulatory networks", Theoretical biology & medical modelling 3, 13 (2006). URL:http://www.tbiomed.com/content/3/1/13
- A. Naldi, J. Carneiro, C. Chaouiya & D. Thieffry, "Diversity and plasticity of Th cell types predicted from regulatory network modelling", PLoS Computational Biology 6, 9 (2010) URL: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000912
- Squad & boolSim
- A. Di Cara, A. Garg, G. De Micheli, I. Xenarios & L. Mendoza, "Dynamic simulation of regulatory networks using SQUAD", BMC Bioinformatics 8, 462 (2007) URL: http://www.biomedcentral.com/1471-2105/8/462
- A. Garg, A. Di Cara, I. Xenarios, L. Mendoza & G. De Micheli, "Synchronous versus asynchronous modeling of gene regulatory networks", Bioinformatics 24, 1917 (2008) URL: http://bioinformatics.oxfordjournals.org/content/24/17/1917
- 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
- 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
