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

by: M Hucka, A Finney, HM Sauro, H Bolouri, JC Doyle, H Kitano, AP Arkin, BJ Bornstein, D Bray, A Cornish-Bowden, AA Cuellar, S Dronov, ED Gilles, M Ginkel, V Gor, II Goryanin, WJ Hedley, TC Hodgman, JH Hofmeyr, PJ Hunter, NS Juty, JL Kasberger, A Kremling, U Kummer, N Le Novère, LM Loew, D Lucio, P Mendes, E Minch, ED Mjolsness, Y Nakayama, MR Nelson, PF Nielsen, T Sakurada, JC Schaff, BE Shapiro, TS Shimizu, HD Spence, J Stelling, K Takahashi, M Tomita, J Wagner, J Wang

Bioinformatics, Vol. 19, No. 4. (1 March 2003), pp. 524-531.

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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/

@article{sbml, 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/}, address = {Control and Dynamical Systems, MC 107-81, California Institute of Technology, Pasadena, CA 91125, USA. sysbio-team@caltech.edu}, author = {Hucka, M. and Finney, A. and Sauro, H. M. and Bolouri, H. and Doyle, J. C. and Kitano, H. and Arkin, A. P. and Bornstein, B. J. and Bray, D. and Cornish-Bowden, A. and Cuellar, A. A. and Dronov, S. and Gilles, E. D. and Ginkel, M. and Gor, V. and Goryanin, I. I. and Hedley, W. J. and Hodgman, T. C. and Hofmeyr, J. H. and Hunter, P. J. and Juty, N. S. and Kasberger, J. L. and Kremling, A. and Kummer, U. and Le Nov\`{e}re, N. and Loew, L. M. and Lucio, D. and Mendes, P. and Minch, E. and Mjolsness, E. D. and Nakayama, Y. and Nelson, M. R. and Nielsen, P. F. and Sakurada, T. and Schaff, J. C. and Shapiro, B. E. and Shimizu, T. S. and Spence, H. D. and Stelling, J. and Takahashi, K. and Tomita, M. and Wagner, J. and Wang, J. }, citeulike-article-id = {781}, doi = {http://dx.doi.org/10.1093/bioinformatics/btg015}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {gochebi, mike-hucka, sbml}, month = {March}, number = {4}, pages = {524--531}, posted-at = {2008-08-06 09:01:55}, priority = {2}, title = {The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.}, url = {http://dx.doi.org/10.1093/bioinformatics/btg015}, volume = {19}, year = {2003} }

RIS record

TY - JOUR ID - sbml L3 - citeulike-article-id:781 TI - The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. JF - Bioinformatics VL - 19 IS - 4 SP - 524 EP - 531 AD - Control and Dynamical Systems, MC 107-81, California Institute of Technology, Pasadena, CA 91125, USA. sysbio-team@caltech.edu SN - 1367-4803 N2 - 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/ KW - gochebi KW - mike-hucka KW - sbml AU - Hucka, M AU - Finney, A AU - Sauro, HM AU - Bolouri, H AU - Doyle, JC AU - Kitano, H AU - Arkin, AP AU - Bornstein, BJ AU - Bray, D AU - Cornish-Bowden, A AU - Cuellar, AA AU - Dronov, S AU - Gilles, ED AU - Ginkel, M AU - Gor, V AU - Goryanin, II AU - Hedley, WJ AU - Hodgman, TC AU - Hofmeyr, JH AU - Hunter, PJ AU - Juty, NS AU - Kasberger, JL AU - Kremling, A AU - Kummer, U AU - Le Novère, N AU - Loew, LM AU - Lucio, D AU - Mendes, P AU - Minch, E AU - Mjolsness, ED AU - Nakayama, Y AU - Nelson, MR AU - Nielsen, PF AU - Sakurada, T AU - Schaff, JC AU - Shapiro, BE AU - Shimizu, TS AU - Spence, HD AU - Stelling, J AU - Takahashi, K AU - Tomita, M AU - Wagner, J AU - Wang, J PY - 2003/03/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btg015 ER -

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