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Systems Biology Markup Language (SBML)

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  • First Online:
Encyclopedia of Computational Neuroscience

Synonyms

SBML

Definition

SBML (the Systems Biology Markup Language, http://sbml.org) is a representation format designed to enable software systems to communicate and store computational models of biological processes. It is not intended as a universal language for quantitative models; rather, SBML’s purpose is to serve as a lingua franca for exchanging the essential aspects of a computational model between widely different software systems and databases.

Detailed Description

A vast number of modeling and simulation software tools are available today for research in biological domains such as computational neuroscience. This wealth of resources is a boon to researchers, but it also presents interoperability problems. Different software tools for systems biology are implemented in different programming languages, run on different operating systems, express models using different mathematical frameworks, provide different analysis methods, present different user interfaces, and support...

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Reference

  • 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 J-HS, 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 JM, Wang J (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524–531

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Author information

Authors and Affiliations

  1. Computing and Mathematical Sciences, California Institute of Technology, 1200 E. California Blvd, 91125, Pasadena, CA, USA

    Michael Hucka

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  1. Michael Hucka
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Corresponding author

Correspondence to Michael Hucka .

Editor information

Editors and Affiliations

  1. Atlanta, Georgia, USA

    Dieter Jaeger

  2. Department of Biomedical Engineering, Florida International University, Miami, Florida, USA

    Ranu Jung

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© 2013 Springer Science+Business Media New York

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Hucka, M. (2013). Systems Biology Markup Language (SBML). In: Jaeger, D., Jung, R. (eds) Encyclopedia of Computational Neuroscience. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7320-6_376-4

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  • DOI: https://doi.org/10.1007/978-1-4614-7320-6_376-4

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  • Publisher Name: Springer, New York, NY

  • Online ISBN: 978-1-4614-7320-6

  • eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences

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