The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

Michael Hucka(California Institute of Technology), Frank Bergmann(California Institute of Technology), Claudine Chaouiya(Centre National de la Recherche Scientifique), Andreas Dräger(German Center for Infection Research), Stefan Hoops, Sarah Keating(European Bioinformatics Institute), Matthias König(Humboldt-Universität zu Berlin), Nicolas Le Novère(Babraham Institute), Chris J. Myers(University of Utah), Brett G. Olivier, Sven Sahle(Heidelberg University), James C. Schaff(University of Connecticut), Rahuman S. Malik‐Sheriff(European Bioinformatics Institute), Lucian P. Smith(University of Washington), Dagmar Waltemath(Universitätsmedizin Greifswald), Darren J. Wilkinson, Fengkai Zhang(National Institutes of Health)
Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics
June 20, 2019
10.1515/jib-2019-0021
Cited by 273Open Access
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Abstract

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

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