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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models |
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| Authors: | Hucka M Finney A Sauro H M Bolouri H Doyle J C Kitano H Arkin A P Bornstein B J Bray D Cornish-Bowden A Cuellar A A Dronov S Gilles E D Ginkel M Gor V Goryanin I I Hedley W J Hodgman T C Hofmeyr J-H Hunter P J Juty N S Kasberger J L Kremling A Kummer U Le Novère N Loew L M Lucio D Mendes P Minch E Mjolsness E D Nakayama Y Nelson M R Nielsen P F Sakurada T Schaff J C Shapiro B E Shimizu T S Spence H D Stelling J Takahashi K Tomita M Wagner J Wang J;SBML Forum |
| Institution: | Control and Dynamical Systems, MC 107-81, California Institute of Technology, Pasadena, CA 91125, USA. sysbio-team@caltech.edu |
| 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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