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

Bioinformatics (Oxford, England) - Tập 19 Số 4 - Trang 524-531 - 2003
Michael Hucka1, Andrew Finney1, Herbert M. Sauro1, Hamid Bolouri2, John C. Doyle3, Anna Zhukova1, Adam P. Arkin4, B. Bornstein5, Dennis Bray6, Athel Cornish‐Bowden7, Autumn Cuellar8, С. М. Дронов9, E. D. Gilles10, Martin Ginkel10, V. Gor5, Igor Goryanin9, Warren Hedley8, Charlie Hodgman9, Jan‐Hendrik S. Hofmeyr11, Peter Hunter8, Nick Juty9, Jay Kasberger4, Andreas Kremling10, Ursula Kummer12, Nicolas Le Novère6, Leslie M. Loew13, Daniel Lucio13, Pedro Mendes14, Eric Minch15, Eric Mjolsness16, Yoichi Nakayama17, M. R. Nelson18, Poul Nielsen8, Takeshi Sakurada17, James C. Schaff13, Bruce E. Shapiro5, Thomas Shimizu6, H. D. Spence9, Jörg Stelling10, Koichi Takahashi17, Masaru Tomita17, Johannes Michael Wagner13, Jun Wang18
1California Institute of Technology, Pasadena, USA
2California Institute of Technology, Pasadena, USA; University of Hertfordshire, Hertfordshire, UK
3California Institute of Technology, Pasadena, USA#TAB#
4University of California, Berkeley, CA, USA
5NASA/JPL, Pasadena, CA, USA
6University of Cambridge, Cambridge, UK
7CNRS-BIP, Marseille, France
8University of Auckland, Auckland, New Zealand
9GlaxoSmithKline, Stevenage, UK
10Systems Biology, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society
11University of Stellenbosch, Stellenbosch, South Africa
12EML, Heidelberg, Germany
13University of Connecticut Health Center, Farmington, CT, USA
14Virginia Bioinformatics Institute, Blacksburg, VA, USA
15LION Bioscience AG, Heidelberg, Germany
16[Sch. of Inf. & Comput. Sci., Univ. of California, Irvine, CA, USA]
17Keio University, Tokyo, Japan
18Physiome Sciences Inc., Princeton, NJ, USA

Tóm tắt

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: [email protected] * To whom correspondence should be addressed.

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Bioinformatics (Oxford, England)

Tập 19 Số 4

524-531

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