Logos : INRIA, INSERM, GDR Spring School on
Dynamical Modelling of
Biological Regulatory Networks
April 9-20 2007, Les Houches, France

The program consists of twelve lectures, each about three hours long, in the morning and early evening. Each lecture combines methodological aspects, concrete applications, and leaves ample time for discussion. The applications are selected so as to enable comparisons between the different modelling approaches.

Practical sessions are devoted to the discovery of specific computer tools (Matlab or Scilab, BIOCHAM, GNA, GINsim, PEP or INA, STOCKS,...) through the analysis of examples introduced in the lectures. In addition, the practical sessions comprise coaching of the mini-projects carried out by groups of 3-5 participants, with a bibliographical review and (tentatively) hands-on computer exercises. The final day is devoted to short presentations of the mini-projects by the students.

Free time should be largely devoted to the mini-projects in small groups, except a few afternoons and Sunday, which are reserved for skiing or sightseeing.
This schedule may be slightly changed during the school so as to take advantage of the best skiing conditions.

Monday 09 April
Evening Introduction

Tuesday 10 April
9:00 - 12:00 B. Vandenbunder
(IRI, Lille)
Primer in molecular and cellular biology: organisation of biological systems, genetic regulation, signal transduction, molecular networks...
   Download : Presentation (.ppt)
14:00 - 17:00 A. Cornish-Bowden
(BIP, Marseille)
Differential equation modelling and analysis of metabolic networks
   Download : Presentation (.pdf)
Evening Questions / Projects

Wednesday 11 April
9:00 - 12:00 A. Ciliberto
(IFOM, Milano)
Dynamical systems I: Differential equations and their applications to the modelling of the regulatory network controlling eukaryote cell cycle
   Download : Presentation (.pdf)
14:00 - 17:00  
Evening D. Kahn (Université Claude Bernard, INRA, INRIA, Lyon) Modularity of biological regulation: how can we model the interplay between gene regulation and metabolic control?
   Download : Presentation (.pdf)

Thursday 12 April
9:00 - 12:00 B. Fernandez
(CPT, Marseille)
Dynamical systems II: Nonlinear applications, symbolic dynamics, application to regulatory circuit engineering
   Download : Paper (.pdf)
14:00 - 17:00  
Evening V. Hakim
(ENS, Paris)
In silico evolution of regulatory networks. Applications to the generation of molecular oscillators.
   Download : Presentation (.pdf)

Friday 13 April
9:00 - 12:00 C. Chaouiya and D. Thieffry
(Université de la Méditerranée, Marseille)
Logical modelling of biological regulatory networks. Applications to gene networks controlling cell cycle, DNA damage repair check- point, and cell differentiation.
   Download : Presentation1 (.pdf) - Presentation2 (.pdf) - Paper (.pdf)
14:00 - 17:00  
Evening F. Fages
(INRIA, Rocquencourt)
Formal verification of dynamical models and application to cell cycle.
   Download : Presentation (.pps) - Paper (.pdf)

Saturday 14 April
9:00 - 12:00 D. Gonze
(Université Libre de Bruxelles)
Stochastic simulations and their application to molecular networks.
   Download : Presentation1 (.pdf) - Presentation2 (.pdf) - Presentation3 (.pdf)
14:00 - 17:00  
Evening L. Tsimring
(University of California, San Diego)
Non-Markovian effects in genetic regulatory networks.
   Download : Presentation (.ppt)

Sunday 15 April
9:00 - 12:00  
14:00 - 17:00  

Monday 16 April
9:00 - 12:00 H. de Jong and D. Ropers
(INRIA, Grenoble)
Dynamical systems III: Piecewise-linear differential equations and application to the regulatory network controlling the stress response in E. coli
   Download : Presentation1 (.ppt) - Presentation2 (.ppt)
14:00 - 17:00 Practical session
Evening Practical session

Tuesday 17 April
9:00 - 12:00 T. Perkins
(McGill University, Montreal)
Inference of regulatory networks from temporal expression time series. Application to the Drosophila segmentation network.
   Download : Presentation1 (.pdf) - Presentation2 (.pdf)
14:00 - 17:00  
Evening Projects

Wednesday 18 April
9:00 - 12:00 Projects
14:00 - 17:00  
Evening Projects

Thursday 19 April
9:00 - 12:00 Presentations
14:00 - 17:00 Presentations
Evening Farewell party

Friday 20 April
9:00 - 12:00 Presentations
14:00 - 17:00 Departure