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2003•BioinformaticsOpen access

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

Michael Hucka, Andrew Finney, Herbert M. Sauro, Hamid Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, B. Bornstein, D. Bray, Athel Cornish‐Bowden, Autumn Cuellar, С. М. Дронов, E. D. Gilles, Martin Ginkel, V. Gor, Igor Goryanin, Warren Hedley, Charlie Hodgman, Jan Hofmeyr, Peter Hunter, Nick Juty, Jay Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, Daniel Lucio, Pedro Mendes, Eric Minch, Eric Mjolsness, Yoichi Nakayama, M. R. Nelson, Poul Nielsen, Takeshi Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Shimizu, H. D. Spence, Joerg Stelling, Koichi Takahashi, Masaru Tomita, J. Wagner, Jian Wang

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Abstract

MOTIVATION: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. AVAILABILITY: The specification of SBML Level 1 is freely available from http://www.sbml.org/

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What this paper is about

MOTIVATION: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. AVAILABILITY: The specification of SBML Level 1 is freely available from http://www.sbml.org/

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Available abstract

MOTIVATION: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. AVAILABILITY: The specification of SBML Level 1 is freely available from http://www.sbml.org/

Key concepts: SBML, Markup language, Systems biology, Computer science, XML, Programming language, Computational biology, Theoretical computer science

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