Logical models; Systems biology; Standards; Qualitative models; Format conversion; SBML; SBML-qual; Systems Biology Markup Language
Abstract :
[en] Logical models are widely used to study regulatory and signaling systems, yet their reuse, annotation, and exchange across tools remain challenging. Although SBML Level 3 Qualitative Models (SBML-qual) provides a standard representation, its XML-based syntax is difficult to inspect and edit directly. Here we introduce TabularQual, a spreadsheet-based, community-driven representation for Boolean and multi-valued logical models, together with a bidirectional converter between spreadsheets and SBML-qual. The converter is accessible programmatically and via a web interface to support diverse user workflows. We further describe two integration strategies that enable existing modeling tools to operate with TabularQual, either through SBML-qual exchange or via direct support. Case studies using the Stress Knowledge Map and CaSQ demonstrate how this integration supports model construction, curation, and reuse. TabularQual provides a practical bridge between human-readable model representations and standardized executable formats, supporting reproducibility, interoperability, and community-driven model development.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Li, Luna Xingyu ; Department of Medical Education and Biomedical Informatics, University of Washington, Seattle, United States
Bleker, Carissa ; Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 121, 1000 Ljubljana, Slovenia
Soliman, Sylvain ; Inria, Saclay Center, Lifeware team, France
Hiroi, Noriko ; Kanagawa Institute of Technology, Keio university school of Medicine
Helikar, Tomáš ; University of Nebraska-Lincoln
König, Matthias ; Humboldt-Universitat zu Berlin, Faculty of Life Science, Institute of Biology, Philippstrasse 13, 10115 Berlin, Germany, University Hospital Schleswig-Holstein, Campus Lubeck, First Department of Medicine, 23538 Lubeck, Germany
Maia Ladeira, Luiz Carlos ; Université de Liège - ULiège > Département d'aérospatiale et mécanique > Génie biomécanique ; Université de Liège - ULiège > GIGA > GIGA Molecular & Computational Biology - Biomechanics Research Unit
Monteiro, Pedro T ; INESC-ID, Lisbon, Portugal, IST - University of Lisbon, Portugal
Noël, Vincent ; Institut Curie, Universite PSL, Paris, France, INSERM, U1331, Paris, France
Pastva, Samuel ; Faculty of Informatics, Masaryk University Botanicka 68a 602 00 Brno Czech Republic
Salazar, Albin; Centre for the Advanced Study of Collective Behaviour and University of Konstanz
Šafránek, David ; Faculty of Informatics, Masaryk University Botanicka 68a 602 00 Brno Czech Republic
Thieffry, Denis ; Departement de Biologie, Ecole Normale Superieure, PSL Universite, Paris, France, Institut Curie, Universite PSL, F-75005, Paris, France
Tsirvouli, Eirini ; Department of Clinical and Molecular Medicine, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
Niarakis, Anna ; Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, UPS, CNRS, Toulouse, France, Lifeware Group, Inria, Saclay-Ile-de-France, Palaiseau, France
Gennari, John ; Department of Medical Education and Biomedical Informatics, University of Washington, Seattle, United States