The systems biology markup language (SBML): a medium for

representation and exchange of biochemical network models (original) (raw)

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Revision received:

15 October 2002

Accepted:

25 October 2002

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M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle, H. Kitano, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. C. Hodgman, J.-H. Hofmeyr, P. J. Hunter, N. S. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Novère, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff, B. E. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, J. Wang, and the rest of the SBML Forum:, The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, Volume 19, Issue 4, March 2003, Pages 524–531, https://doi.org/10.1093/bioinformatics/btg015
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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/

Contact: sysbio-team@caltech.edu

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© Oxford University Press 2003

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