W08 - Workshop on Logical Modelling and Analysis of Cellular Networks

Workshop scope

Since the seminal publications of Stuart Kauffman and Ren√© Thomas about 40 years ago, logical modelling has been increasingly used to model the dynamical behaviour of biological regulatory networks. However, behind the common denomination ‚Äúlogical modelling‚ÄĚ, computational biologists are using different formalisations (Boolean, multilevel, deterministic, stochastic, etc.) and have developed various methods and tools, which might be somewhat difficult to choose from to address specific biological questions.
This workshop proposal aims at providing an extensive and organised overview of recent developments that render possible the modelling and the analysis of large cellular networks, encompassing various signalling pathways, sophisticate transcriptional networks, as well as novel regulatory mechanisms (e.g. regulatory effects of miRNA, epigenetic regulations, etc.).
Speakers will refer to applications dealing with the control of cell proliferation, cell differentiation and reprogramming, embryonic development, immune response, and cancer drug resistance. They will emphasise the biological insights gained with logical modelling in general, as well as by using specific analysis methods.

Target audience

Students and researchers interested in modelling approaches to tackle the complexity of regulatory and signalling networks.

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9h00-10h30 - Chair: Ioannis Xenarios (Lausanne, Switzerland)
- Denis Thieffry (Paris, France): Introduction
- Julio Saez-Rodriguez (Hinxton, UK): Logic models of signalling networks from phosphoproteomic data
- Tomas Helikar (Lincoln, Nebraska, USA): A collaborative and crowd-sourcing approach to the construction and analysis of logical models

10h30-11h00 - Coffee break

11h00-12h30 - Chair: Claudine Chaouiya (Oeiras, Portugal)
- Reinhard Laubenbacher (Blacksburg, Virginia, USA): Steady analysis of Boolean network models through model reduction and computational algebra
- Reka Albert (State College, Pennsylvania, USA): Logic network allows the determination and control of cellular attractors
- Heike Siebert (Berlin, Germany): Logical network analysis with symbolic steady states

12h30-14h00 Lunch break

14h00-15h30 - Chair: Anne Siegel (Rennes, France) 
- Wassim Abou-Jaoude (Paris, France): Logical modeling of T-helper cell differentiation and plasticity
- Louis Filipo Fitime (Nantes, France): Integrating time-series data on large-scale cell-based models: application to skin differentiation
- Adrien Fauré (Yamaguchi, Japan): A discrete model of Drosophila eggshell patterning reveals cell-autonomous and juxtacrine effects

15h30-16h - Coffee break

16h00-17h00 - Chair: Tomas Helikar (Lincoln, Nebraska, USA) 
- Siegel Anne (Rennes, France): Improving robustness in the study of logical model of signalling networks with answer set programming
- Gautier Stoll (Paris, France): Continuous time Boolean modeling with MaBoSS software: algorithm and applications

17h00-18h - Chair: Denis Thieffry (Paris, France) - General discussion and conclusions

Date and venue

This workshop will be held on Saturday, September 6th, 2014 (all day). Note that this workshop is coupled with the tutorial "Computational Tools to Define and Analyse Logical Models of Cellular Networks", on the following day (Sunday, September 7th, 2014).

For information about the venue, we refer to ECCB'14 corresponding page.


  • Denis Thieffry (Ecole Normale Sup√©rieure, France)
  • Ioannis Xenarios (Swiss Institute of Bioinformatics, Switzerland)

Scientific committee

  • Bockmayr Alexander
  • Chaouiya Claudine
  • Fages Fran√ßois
  • Helikar Tomas
  • Saez-Rodriguez Julio
  • Thieffry Denis
  • Xenarios Ioannis





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