Bioinformatics

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Bioinformatics Vol. 19 no. 4 2003
Pages 524-531
© 2003 Oxford University Press

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

M. Hucka ^1,2,*, A. Finney ^1,2, H. M. Sauro ^1,2, H. Bolouri ^1,2,3, J. C. Doyle ¹, H. Kitano ^1,2,4,16,18, and the rest of the SBML Forum:, A. P. Arkin ⁵, B. J. Bornstein ⁶, D. Bray ⁷, A. Cornish-Bowden ⁸, A. A. Cuellar ⁹, S. Dronov ¹⁰, E. D. Gilles ¹¹, M. Ginkel ¹¹, V. Gor ⁶, I. I. Goryanin ¹⁰, W. J. Hedley ⁹, T. C. Hodgman ¹⁰, J.-H. Hofmeyr ¹², P. J. Hunter ⁹, N. S. Juty ¹⁰, J. L. Kasberger ⁵, A. Kremling ¹¹, U. Kummer ¹³, N. Le Novère ⁷, L. M. Loew ¹⁴, D. Lucio ¹⁴, P. Mendes ¹⁵, E. Minch ¹⁹, E. D. Mjolsness ²⁰, Y. Nakayama ¹⁶, M. R. Nelson ¹⁷, P. F. Nielsen ⁹, T. Sakurada ¹⁶, J. C. Schaff ¹⁴, B. E. Shapiro ⁶, T. S. Shimizu ⁷, H. D. Spence ¹⁰, J. Stelling ¹¹, K. Takahashi ¹⁶, M. Tomita ¹⁶, J. Wagner ¹⁴ and J. Wang ¹⁷

¹ Control and Dynamical Systems, MC 107-81, California Institute of Technology, Pasadena, CA 91125, USA
² ERATO Kitano Symbiotic Systems Project, Tokyo, Japan
³ University of Hertfordshire, Hertfordshire, UK
⁴ The Systems Biology Institute, Tokyo, Japan
⁵ University of California, Berkeley, CA, USA
⁶ NASA JPL, Pasadena, CA, USA
⁷ University of Cambridge, Cambridge, UK
⁸ CNRS-BIP, Marseille, France
⁹ University of Auckland, Auckland, New Zealand
¹⁰ GlaxoSmithKline, Stevenage, UK
¹¹ Max-Planck-Institute for Complex Technical Systems, Magdeburg, Germany
¹² University of Stellenbosch, Stellenbosch, South Africa
¹³ EML, Heidelberg, Germany
¹⁴ University of Connecticut Health Center, Farmington, CT, USA
¹⁵ Virginia Bioinformatics Institute, Blacksburg, VA, USA
¹⁶ Keio University, Tokyo, Japan
¹⁷ Physiome Sciences Inc., Princeton, NJ, USA
¹⁸ Sony Computer Science Laboratories, Inc., Tokyo, Japan
¹⁹ LION bioscience AG, Heidelberg, Germany
²⁰ School of Information and Computer Science, University of California, Irvine, CA, USA

Received on May 17, 2002 ; revised on October 15, 2002 ; accepted on October 25, 2002

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{at}caltech.edu

^* To whom correspondence should be addressed.

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