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

Michael Hucka¹, Frank T Bergmann¹, Claudine Chaouiya², Andreas Dräger^{3

4

5}, Stefan Hoops⁶, Sarah M Keating⁷, Matthias König⁸, Nicolas Le Novère⁹, Chris J Myers¹⁰, Brett G Olivier¹¹, Sven Sahle¹², James C Schaff¹³, Rahuman Sheriff⁷, Lucian P Smith¹⁴, Dagmar Waltemath¹⁵, Darren J Wilkinson¹⁶, Fengkai Zhang¹⁷

Affiliations

¹ California Institute of Technology, Pasadena, CA, USA.
² Aix-Marseille University, CNRS, I2M, Marseille, France.
³ Department of Computer Science, University of Tübingen, Tübingen, Germany.
⁴ Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany.
⁵ German Center for Infection Research (DZIF), Tübingen, Germany.
⁶ Virginia Bioinformatics Institute, Blacksburg, VA, USA.
⁷ European Bioinformatics Institute, Cambridge, UK.
⁸ Humboldt University Berlin, Berlin, Germany.
⁹ Babraham Institute, Cambridge, UK.
¹⁰ University of Utah, Salt Lake City, UT, USA.
¹¹ VU University Amsterdam, Amsterdam, Netherlands.
¹² University of Heidelberg, Heidelberg, Germany.
¹³ University of Connecticut, Storrs, CT, USA.
¹⁴ University of Washington, Seattle, WA, USA.
¹⁵ University Medicine Greifswald, Greifswald, Germany.
¹⁶ Newcastle University, Newcastle, Germany.
¹⁷ NIAID/NIH, Bethesda, MD, USA.

PMID: 31219795
PMCID: PMC6798823
DOI: 10.1515/jib-2019-0021

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

Michael Hucka et al. J Integr Bioinform. 2019.

. 2019 Jun 20;16(2):20190021.

doi: 10.1515/jib-2019-0021.

Authors

Affiliations

¹ California Institute of Technology, Pasadena, CA, USA.
² Aix-Marseille University, CNRS, I2M, Marseille, France.
³ Department of Computer Science, University of Tübingen, Tübingen, Germany.
⁴ Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany.
⁵ German Center for Infection Research (DZIF), Tübingen, Germany.
⁶ Virginia Bioinformatics Institute, Blacksburg, VA, USA.
⁷ European Bioinformatics Institute, Cambridge, UK.
⁸ Humboldt University Berlin, Berlin, Germany.
⁹ Babraham Institute, Cambridge, UK.
¹⁰ University of Utah, Salt Lake City, UT, USA.
¹¹ VU University Amsterdam, Amsterdam, Netherlands.
¹² University of Heidelberg, Heidelberg, Germany.
¹³ University of Connecticut, Storrs, CT, USA.
¹⁴ University of Washington, Seattle, WA, USA.
¹⁵ University Medicine Greifswald, Greifswald, Germany.
¹⁶ Newcastle University, Newcastle, Germany.
¹⁷ NIAID/NIH, Bethesda, MD, USA.

PMID: 31219795
PMCID: PMC6798823
DOI: 10.1515/jib-2019-0021

Abstract

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. 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 Release 2 of Version 2 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. Release 2 corrects some errors and clarifies some ambiguities discovered in Release 1. 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 website at http://sbml.org/.

Keywords: Representation; Standards; Systems Biology Markup Language; Visualization.

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

Affiliations

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

Authors

Affiliations

Abstract

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