The systems biology markup language (SBML): a medium forrepresentation and exchange of biochemical network models
Michael Hucka(California Institute of Technology), Andrew Finney(California Institute of Technology), Herbert M. Sauro(California Institute of Technology), Hamid Bolouri(California Institute of Technology), John C. Doyle(California Institute of Technology), Hiroaki Kitano(California Institute of Technology), Adam P. Arkin(University of California, Berkeley), B. Bornstein, D. Bray(University of Cambridge), Athel Cornish‐Bowden(Centre National de la Recherche Scientifique), Autumn Cuellar(University of Auckland), С. М. Дронов(Age UK), E. D. Gilles(Max Planck Society), Martin Ginkel(Max Planck Society), V. Gor, Igor Goryanin(Age UK), Warren Hedley(University of Auckland), Charlie Hodgman(Age UK), Jan Hofmeyr(Stellenbosch University), Peter Hunter(University of Auckland), Nick Juty(Age UK), Jay Kasberger(University of California, Berkeley), Andreas Kremling(Max Planck Society), Ursula Kummer(European Media Laboratory (Germany)), Nicolas Le Novère(University of Cambridge), Leslie M. Loew(UConn Health), Daniel Lucio(UConn Health), Pedro Mendes, Eric Minch, Eric Mjolsness(University of California, Irvine), Yoichi Nakayama(Keio University), M. R. Nelson, Poul Nielsen(University of Auckland), Takeshi Sakurada(Keio University), James C. Schaff(UConn Health), Bruce E. Shapiro, Thomas Shimizu(University of Cambridge), H. D. Spence(Age UK), Joerg Stelling(Max Planck Society), Koichi Takahashi(Keio University), Masaru Tomita(Keio University), J. Wagner(UConn Health), Jian Wang
Cited by 3,148Open Access
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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