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ICSB´15 Tutorial on Logical Modelling, November 26, Singapore

Workshop, program and slides

Instructors' contact:

  • Prof. Claudine CHAOUIYA, Instituto Gulbenkian de Ciência, Oeiras, Portugal ()​​​​​​​​​
  • Assist. Prof. Tomas HELIKAR, University of Nebraska – Lincoln, USA ()​

Venue

The tutorial will take place in Block MD1(MD1-08-01E and MD1-08-03E) at Yong Loo Lin School of Medicine, National University of Singapore (NUS). The nearest train station is Kent Ridge Station on the Circle line, see direction at https://www.sph.nus.edu.sg/contact.

Program

Following a brief introduction to the modelling framework, hands-on sessions will be organised in parallel sessions. The introductory part intends to provide the participants with the concepts necessary for both hands-on sessions with the software tools GINsim and the Cell Collective. Participants should come with their own laptops.
Download Tutorial description

Please check material and instructions for GINsim and CellCollective hands-on session.

  • 14:00 - 14:30 Introduction (room MD1-08-01E) Slides
  • 14:40 - 16:10 GINsim, Cell Collective (parallel sessions)
  • 16:10 - 16:20 Break
  • 16:30 - 18:00 GINsim, Cell Collective (parallel sessions)


GINsim

GINsim is OS independent (Linux, Mac OS 10.3+, Windows). In order to run the latest GINsim modelling and simulation tool, JAVA version 1.6 or higher is required. It is advisable that participants download GINsim-2.9.3-with-deps.jar at download page of GINsim web site in advance.

Slides

Part 1:

This part consists in reconstructing and analysing the model of the phage lambda core regulatory network controlling the lysis ­lysogeny decision[6], following most of the content of the chapter [2]. See details and instructions for this first part.

Part 2:

This part consists in a demo of some advanced GINsim functionalities, performing analyses of Mendoza's model for Th cell differentiation [5]. Participants will be able to analyse this or other models.

Cell Collective

The tool is available at dev.cellcollective.org.

Building a model of the Lac Operon with the Cell Collective, see description

References

  • [1] D. Bérenguier et al.(2013) Dynamical modeling and analysis of large cellular regulatory networks , Chaos 23, 025114, DOI

  • [2] C. Chaouiya, A. Naldi and D. Thieffry (2012) Logical Modelling of Gene Regulatory Networks with GINsim, Methods in Molecular Biology, 1, Volume 804, Bacterial Molecular Networks, Part 3, Pages 463­479,DOI pdf

  • [3] Helikar T., Kowal B., McClenathan S., Bruckner M., Rowley T., Madrahimov A., Wicks B., Shrestha M., Limbu K., and Rogers J.A. (2012) The Cell Collective: Toward an open and collaborative approach to systems biology. BMC Systems Biology. 6:96 DOI

  • [4] Helikar T., Kowal B., Madrahimov A., Shrestha M., Pedersen J., Konvalina J., and Rogers J.A. (2012) Bio­Logic Builder: A non­technical tool for building dynamical, qualitative models. PLoS ONE 7(10): e46417 DOI

  • [5] Mendoza L. (2006) A network model for the control of the differentiation process in Th cells. Biosystems, Vol 84, Issue 2, pp. 101-114 DOI pdf

  • [6] Thieffry D, Thomas R. (1995) Dynamical behaviour of biological regulatory networks, II. Immunity control in bacteriophage lambda. Bull Math Biol, 57(2):277–297,DOI pdf