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First meeting Common Logical Modelling Toolbox (CoLoMoTo)

IGC, Instituto Gulbenkian de Ciência, Oeiras, Portugal
18-19 November 2010
contact:

Sponsored by

 Instituto Gulbenkian de Ciência European Network of Excellence ENFIN French Embassy in PortugalCâmara Municipal de Oeiras

Notes:

The meeting aims at setting up a consortium to provide a common toolbox, taking advantage of the different existing sofwares, gathering key players in the development of tools for discrete modelling of biological networks. The goal is to define a network of research groups working on qualitative modelling of biological pathways. With this network, we will be able to apply for international financial supports and to ensure a better visibility of this research topic. A joint development of a software platform will certainly provide the community with a valuable and maintained software suite.

Practical information for participants...

Program

Thurday, 18
  • 14:00-14:15 - C. Chaouiya: welcoming and brief overview of qualitative modelling formalisms, similarities and differences
  • 14:15-14:45 - A. Naldi: GINsim, implementation and functionalities
  • 14:45-15:20 - T. Helikar: Chemchains, implementation and functionalities
  • 15:20-15:40 - A. Zinovyev: Binom, implementation and functionalities
  • 15:40-16:10 - Coffea break
  • 16:10-16:30 - J. Wu: CellNetOptimizer, implementation and functionalities
  • 16:30-17:00 - A. Von Kamp: CellNetAnalyzer, implementation and functionalities
  • 17:00-17:30 - I. Xenarios: Squad, implementation and functionalities
  • 17:30-17:45 - I. Xenarios: Biocuration
  • 17:45-18:15 - P. Monteiro: GNA, model checking
  • 18:15-19:00 - open discussion
  • 19:00 Cocktail
Friday, 19
  • 10:00-10:20 - B. Schwikowski: Cytoscape, a succesful story!
  • 10:20-10:45 C. Chaouiya, D. Berenguier: SBML Level 3 quali package
  • 10:40 -11:00 - Coffea break
  • 11:00 - 12:00 - General discussion, objectives and strategy
  • 12:00-14:30 - IGC seminar + Lunch
  • 14:30-16:30 - Round table on technical issues and strategies - conclusions

Participants

  • 1 Duncan Berenguier TAGC, IML, Marseille, FR
  • 2 Jorge Carneiro IGC Oeiras PT
  • 3 Claudine Chaouiya IGC Oeiras PT
  • 4 Tomas Helikar University of Nebraska USA
  • 5 Pedro Monteiro IMM Lisboa PT
  • 6 Aurélien Naldi CIG Lausanne, CH
  • 7 Anne Niknejad ISB-SIB Lausanne, CH
  • 8 Manuel Pita IGC Oeiras PT
  • 9 Martial Sankar ISB-SIB Lausanne, CH
  • 10 Benno Schwikowski Pasteur, Paris FR
  • 11 Denis Thieffry ENS, Paris FR
  • 12 Laurent Tichit IML Marseille FR
  • 13 Axel Von Kamp MPI Magdeburg, DE
  • 14 Jerry Wu EBI Cambridge, UK
  • 15 Ioannis Xenarios ISB-SIB Lausanne, CH
  • 16 Andrei Zynoviev Curie, Paris, FR