title: Cooperative development of logical modelling standards and tools with CoLoMoTo.
abstract: The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches. Indeed, models can help elucidate properties of these networks, understand their behaviour and provide (testable) predictions by performing in silico experiments. In this context, qualitative, logical frameworks have emerged as relevant approaches, as demonstrated by a growing number of published models, along with new methodologies and software tools. This productive activity now requires a concerted effort to ensure model reusability and interoperability between tools. Following an outline of the logical modelling framework, we present the most important achievements of the Consortium for Logical Models and Tools, along with future objectives. Our aim is to advertise this open community, which welcomes contributions from all researchers interested in logical modelling or in related mathematical and computational developments.
authors.affiliation: Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Naldi
authors.affiliation: Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA.
authors.forename: Pedro T
authors.initials: PT
authors.lastname: Monteiro
authors.affiliation: Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA.
authors.forename: Christoph
authors.initials: C
authors.lastname: Müssel
authors.affiliation: Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Res
authors.forename: Hans A
authors.initials: HA
authors.lastname: Kestler
authors.affiliation: Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA.
authors.forename: Denis
authors.initials: D
authors.lastname: Thieffry
authors.affiliation: Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.affiliation: Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA.
authors.forename: Julio
authors.initials: J
authors.lastname: Saez-Rodriguez
authors.affiliation: Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA.
authors.forename: Tomas
authors.initials: T
authors.lastname: Helikar
authors.affiliation: Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA.
authors.forename: Claudine
authors.initials: C
authors.lastname: Chaouiya
mesh_terms: D000818:Animals; D002477:Cells / Q000378:metabolism*; D003198:Computer Simulation; D006801:Humans; D053858:Metabolic Networks and Pathways; D008962:Models, Theoretical; D012958:Societies, Scientific; D012984:Software / Q000592:standards*; D049490:Systems Biology / Q000379:methods