Software tools

• GINsim (Gene Interaction Network simulation), a softare for the modelling, analysis and simulation of signalling and regulatory networks, based on the logical formalism.
• EpiLog (Epithelium Logical Modelling), a software tool for the deminition and simulation of cellular automata over hexagonal cells, extending the logical formalism to multi-cellular networks.

Community resources

• CoLoMoTo (Consortium for Logical Models and Tools), the consortium of research groups interested in logical modelling: modelers, curators and developers of methods and tools.
• SBML (Systems Biology Markup Language), a free and open interchange format for computer models of biological processes.
• COMBINE (COmputational Modeling in BIology' NEtwork), an initiative to coordinate the development of the various community standards and formats for computational models.
• SYSMOD (Computational Modeling of Biological Systems), a Community of Special Interest (COSI) of the International Society for Computational Biology (ISCB). This is a forum for discussion about the combined use of systems biology modeling and bioinformatics to understand biology and disease.

Main collaborators

• Logical modelling
  • Pedro T. Monteiro at INESC-ID, Lisbon University.
  • Denis Thieffry at Ecole Normale Supérieure de Paris (IBENS, ENS).
  • Elisabeth Remy at the Mathematics Institute of Marseille (I2M), MABioS team.
• Cancer networks
  • Laurence Calzone at Institut Curie, Paris.
  • Florence Janody at Instituto de Investigação e Inovação em Saúde, i3S - Porto University.
  • Carla Oliveira at Instituto de Investigação e Inovação em Saúde, i3S - Porto University.
• Developmental biology
  • Lucas Sánchez at the Biological Research Center (Centro de Investigaciones Biológicas, CSIC), Madrid.
  • Elio Sucena at Instituto Gulbenkian de Ciência.
• Regulatory networks in yeasts
  • Miguel C. Teixeira at Institute for Bioengineering and Biosciences, IST, Lisbon University.