{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:39Z","timestamp":1772138079032,"version":"3.50.1"},"reference-count":84,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n                  <jats:p>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.<\/jats:p>\n                  <jats:p>Contact: \u00a0contact@colomoto.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv013","type":"journal-article","created":{"date-parts":[[2015,1,25]],"date-time":"2015-01-25T20:18:20Z","timestamp":1422217100000},"page":"1154-1159","source":"Crossref","is-referenced-by-count":79,"title":["Cooperative development of logical modelling standards and tools with CoLoMoTo"],"prefix":"10.1093","volume":"31","author":[{"given":"Aur\u00e9lien","family":"Naldi","sequence":"first","affiliation":[{"name":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"}]},{"given":"Pedro T.","family":"Monteiro","sequence":"additional","affiliation":[{"name":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"},{"name":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"}]},{"given":"Christoph","family":"M\u00fcssel","sequence":"additional","affiliation":[{"name":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"}]},{"name":"the Consortium for Logical Models and Tools","sequence":"additional","affiliation":[]},{"given":"Hans A.","family":"Kestler","sequence":"additional","affiliation":[{"name":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"},{"name":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"},{"name":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"}]},{"given":"Denis","family":"Thieffry","sequence":"additional","affiliation":[{"name":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"}]},{"given":"Ioannis","family":"Xenarios","sequence":"additional","affiliation":[{"name":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"},{"name":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"}]},{"given":"Julio","family":"Saez-Rodriguez","sequence":"additional","affiliation":[{"name":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID), Lisbon, Portugal, 3Instituto Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"}]},{"given":"Tomas","family":"Helikar","sequence":"additional","affiliation":[{"name":"1 Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, 2Instituto de Engenharia de Sistemas e Computadores-Investiga\u00e7\u00e3o e 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Gulbenkian de Ci\u00eancia (IGC), Oeiras, Portugal, 4Medical Systems Biology, Ulm University, Germany, 5Friedrich-Schiller University Jena, Jena, Germany, 6Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, 7Institut de Biologie de l\u2019\u00c9cole Normale Sup\u00e9rieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, 8Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, 9European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and 10Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA"}]}],"member":"286","published-online":{"date-parts":[[2015,1,25]]},"reference":[{"key":"2023051309143383400_btv013-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0022-5193(03)00035-3","article-title":"The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila 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