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
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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