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

M. Hucka; A. Finney; H. M. Sauro; H. Bolouri; J. C. Doyle; H. Kitano; A. P. Arkin; B. J. Bornstein; D. Bray; A. Cornish-Bowden; A. A. Cuellar; S. Dronov; E. D. Gilles; M. Ginkel; V. Gor; I. I. Goryanin; W. J. Hedley; T. C. Hodgman; J. H. Hofmeyr; P. J. Hunter; N. S. Juty; J. L. Kasberger; A. Kremling; U. Kummer; N. Le Novère; L. M. Loew; D. Lucio; P. Mendes; E. Minch; E. D. Mjolsness; Y. Nakayama; M. R. Nelson; P. F. Nielsen; T. Sakurada; J. C. Schaff; B. E. Shapiro; T. S. Shimizu; H. D. Spence; J. Stelling; K. Takahashi; M. Tomita; J. Wagner; J. Wang

doi:10.1093/bioinformatics/btg015

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

M. Hucka
, A. Finney
, H. M. Sauro
, H. Bolouri
, J. C. Doyle
, H. Kitano
, A. P. Arkin
, B. J. Bornstein
, D. Bray
, A. Cornish-Bowden
, A. A. Cuellar
, S. Dronov
, E. D. Gilles
, M. Ginkel
, V. Gor
, I. I. Goryanin
, W. J. Hedley
, T. C. Hodgman
, J. H. Hofmeyr
, P. J. Hunter

N. S. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Novère, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff, B. E. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, J. Wang

California Institute of Technology
JST-ICORP Computational Brain Project
University of Hertfordshire
The Systems Biology Institute
Keio University
Sony Computer Sci. Laboratories Inc.
University of California at Berkeley
Jet Propulsion Laboratory
University of Cambridge
Institut de Neurosciences de la Timone, Centre National de la Recherche Scientifique - Aix-Marseille University
University of Auckland
Cellzome GmbH
Max Planck Institute for Dynamics of Complex Technical Systems
Stellenbosch University
Univ. of Connecticut Health Center
Virginia BioInformatics Institute
LION Bioscience AG
University of California, Irvine
Physiome Sciences

Research output: Contribution to journal › Article › peer-review

2452 Scopus citations

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.

Original language	English
Pages (from-to)	524-531
Number of pages	8
Journal	Bioinformatics
Volume	19
Issue number	4
DOIs	https://doi.org/10.1093/bioinformatics/btg015
State	Published - 1 Mar 2003
Externally published	Yes

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10.1093/bioinformatics/btg015

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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., ... Wang, J. (2003). The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics, 19(4), 524-531. https://doi.org/10.1093/bioinformatics/btg015

@article{dab015abfbe5454dbb3076d32b93f03d,

title = "The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models",

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.",

author = "M. Hucka and A. Finney and Sauro, \{H. M.\} and H. Bolouri and Doyle, \{J. C.\} and H. Kitano and Arkin, \{A. P.\} and Bornstein, \{B. J.\} and D. Bray and A. Cornish-Bowden and Cuellar, \{A. A.\} and S. Dronov and Gilles, \{E. D.\} and M. Ginkel and V. Gor 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 A. Kremling and U. Kummer and \{Le Nov{\`e}re\}, N. and Loew, \{L. M.\} and D. Lucio and P. Mendes and E. Minch and Mjolsness, \{E. D.\} and Y. Nakayama and Nelson, \{M. R.\} and Nielsen, \{P. F.\} and T. Sakurada and Schaff, \{J. C.\} and Shapiro, \{B. E.\} and Shimizu, \{T. S.\} and Spence, \{H. D.\} and J. Stelling and K. Takahashi and M. Tomita and J. Wagner and J. Wang",

note = "Funding Information: This work has been supported by: the Japan Science and Technology Corporation{\textquoteright}s ERATO Kitano Symbiotic Systems Project; an International Joint Research Grant from the NEDO/Japanese Ministry of Economy, Trade and Industry; and the Rice Genome and Simulation Project from the Japanese Ministry of Agriculture. Funding Information: The current inability to exchange models between different simulation and analysis tools has its roots in the lack of a common format for describing models. To address this, we formed a Software Platforms for Systems Biology forum under the auspices of the ERATO Kitano Systems Biology Project (funded by the Japan Science and Technology Corporation and hosted in part at the California Institute of Technology). The forum initially included representatives from the teams developing the software packages BioSpice (Arkin, 2001), Cellerator (Shapiro and Mjolsness, 2001), DBsolve (Goryanin et al., 1999), E-CELL (Tomita et al., 2001), Gepasi (Mendes, 1997), Jarnac (Sauro, 2000), StochSim (Morton-Firth and Bray, 1998), and Virtual Cell (Schaff et al., 2001), and later grew to include the developers of ProMoT/DIVA (Ginkel et al., 2000) and the CellML language at the University of Auckland and Physiome Sciences (Hedley et al., 2001).",

year = "2003",

month = mar,

day = "1",

doi = "10.1093/bioinformatics/btg015",

language = "English",

volume = "19",

pages = "524--531",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "4",

}

Hucka, M, Finney, A, Sauro, HM, Bolouri, H, Doyle, JC, Kitano, H, Arkin, AP, Bornstein, BJ, Bray, D, Cornish-Bowden, A, Cuellar, AA, Dronov, S, Gilles, ED, Ginkel, M, Gor, V, Goryanin, II, Hedley, WJ, Hodgman, TC, Hofmeyr, JH, Hunter, PJ, Juty, NS, Kasberger, JL, Kremling, A, Kummer, U, Le Novère, N, Loew, LM, Lucio, D, Mendes, P, Minch, E, Mjolsness, ED, Nakayama, Y, Nelson, MR, Nielsen, PF, Sakurada, T, Schaff, JC, Shapiro, BE, Shimizu, TS, Spence, HD, Stelling, J, Takahashi, K, Tomita, M, Wagner, J & Wang, J 2003, 'The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models', Bioinformatics, vol. 19, no. 4, pp. 524-531. https://doi.org/10.1093/bioinformatics/btg015

TY - JOUR

T1 - The systems biology markup language (SBML)

T2 - A medium for representation and exchange of biochemical network models

AU - Hucka, M.

AU - Finney, A.

AU - Sauro, H. M.

AU - Bolouri, H.

AU - Doyle, J. C.

AU - Kitano, H.

AU - Arkin, A. P.

AU - Bornstein, B. J.

AU - Bray, D.

AU - Cornish-Bowden, A.

AU - Cuellar, A. A.

AU - Dronov, S.

AU - Gilles, E. D.

AU - Ginkel, M.

AU - Gor, V.

AU - Goryanin, I. I.

AU - Hedley, W. J.

AU - Hodgman, T. C.

AU - Hofmeyr, J. H.

AU - Hunter, P. J.

AU - Juty, N. S.

AU - Kasberger, J. L.

AU - Kremling, A.

AU - Kummer, U.

AU - Le Novère, N.

AU - Loew, L. M.

AU - Lucio, D.

AU - Mendes, P.

AU - Minch, E.

AU - Mjolsness, E. D.

AU - Nakayama, Y.

AU - Nelson, M. R.

AU - Nielsen, P. F.

AU - Sakurada, T.

AU - Schaff, J. C.

AU - Shapiro, B. E.

AU - Shimizu, T. S.

AU - Spence, H. D.

AU - Stelling, J.

AU - Takahashi, K.

AU - Tomita, M.

AU - Wagner, J.

AU - Wang, J.

N1 - Funding Information: This work has been supported by: the Japan Science and Technology Corporation’s ERATO Kitano Symbiotic Systems Project; an International Joint Research Grant from the NEDO/Japanese Ministry of Economy, Trade and Industry; and the Rice Genome and Simulation Project from the Japanese Ministry of Agriculture. Funding Information: The current inability to exchange models between different simulation and analysis tools has its roots in the lack of a common format for describing models. To address this, we formed a Software Platforms for Systems Biology forum under the auspices of the ERATO Kitano Systems Biology Project (funded by the Japan Science and Technology Corporation and hosted in part at the California Institute of Technology). The forum initially included representatives from the teams developing the software packages BioSpice (Arkin, 2001), Cellerator (Shapiro and Mjolsness, 2001), DBsolve (Goryanin et al., 1999), E-CELL (Tomita et al., 2001), Gepasi (Mendes, 1997), Jarnac (Sauro, 2000), StochSim (Morton-Firth and Bray, 1998), and Virtual Cell (Schaff et al., 2001), and later grew to include the developers of ProMoT/DIVA (Ginkel et al., 2000) and the CellML language at the University of Auckland and Physiome Sciences (Hedley et al., 2001).

PY - 2003/3/1

Y1 - 2003/3/1

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.

AB - 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.

UR - https://www.scopus.com/pages/publications/0037342537

U2 - 10.1093/bioinformatics/btg015

DO - 10.1093/bioinformatics/btg015

M3 - Article

C2 - 12611808

AN - SCOPUS:0037342537

SN - 1367-4803

VL - 19

SP - 524

EP - 531

JO - Bioinformatics

JF - Bioinformatics

IS - 4

ER -

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

Abstract

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