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Publications

The following are published papers and chapters describing SBML and core SBML supporting tools (e.g. libraries). Please note that none of these publications is normative in the sense of defining SBML. These papers and chapters only provide context and perspectives about SBML and its development. Only the SBML specification documents are normative.

This page does not cover associated standards to use in conjunction with SBML. Please consult the documentation of the COMBINE initiative for entries point to relevant documentation. This page does not cover end-user software either. Visit the SBML software guide for more information on tools supporting SBML.

Publications describing SBML

SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
Chaouiya, Claudine, Berenguier, Duncan, Keating, Sarah M., Naldi, Aurelien, van Iersel, Martijn P., Rodriguez, Nicolas, Dräger, Andreas, Büchel, Finja, Cokelaer, Thomas, Kowal, Bryan, Wicks, Benjamin, Gonçalves, Emmanuel, Dorier, Julien, Page, Michel, Monteiro, Pedro T., von Kamp, Axel, Xenarios, Ioannis, de Jong, Hidde, Hucka, Michael, Klamt, Steffen, Thieffry, Dennis, Le Novère, Nicolas, Saez-Rodriguez, Julio, Helikar, Tomas
Paper published in BMC Systems Biology 7:135, 2013.
A paper describing a format for storing qualitative models such as logical model or some Petri Net models.
Supporting SBML as a Model Exchange Format in Software Applications
Keating, Sarah M., Le Novère, Nicolas
Chapter published in In Silico Systems Biology - Methods in Molecular Biology, Volume 1021, pp 201-225, Springer, 2013.
This chapter describes SBML from its origins, the rationale behind and importance of having a common language to represent models, the development of SBML and outlines the structure of an SBML model. It provides a section on libSBML and a description of the SBML Toolbox.
Software Infrastructure for Effective Communication and Reuse of Computational Models
Finney, Andrew, Hucka, Michael, Bornstein, Benjamin J., Keating, Sarah M., Shapiro, Bruce M., Matthews, Joanne, Kovitz, Benjamin K., Schilstra, Maria J., Funahashi, Akira, Doyle, John, and Kitano, Hiroaki
Chapter published in System Modeling in Cell Biology: From Concepts to Nuts and Bolts, eds. Zoltan Szallasi, Jörg Stelling, and Vipul Periwal, MIT Press, 2006.
This chapter overviews the SBML project and its general goals, and some of the motivations for approaches taken in the development of libSBML. (Note: this is a portion of the chapter; we highly recommend getting the whole book rather than only using this excerpt.)
A model diagram layout extension for SBML
Gauges, Ralph, Rost, Ursula, Sahle, Sven and Wegner, Katia
Paper published in Bioinformatics 22(15):1879–1885, 2006.
A paper describing a proposed format for storing diagrammatic representations of models directly in an SBML model file or data stream. In SBML Level 2, applications can use it by storing the data in SBML <annotation> elements, and for Level 3, it is expected to be turned into a full package, with the same constructs appearing at the top level instead of inside <annotation> elements.
Escalating model sizes and complexities call for standardized forms of representation
Hucka, Michael, and Finney, Andrew
Paper published in Molecular Systems Biology, doi:10.1038/msb4100015, 2005.
Comment paper about the increasingly larger and more complex models being developed by researchers, and the need to standardize representations at different levels for effective communication and sharing of those models.
Developing SBML beyond level 2: proposals for development
Finney, Andrew
Chapter published in Lecture Notes in Computer Science, Vol. 3082, eds. Vincent Danos and Vincent Schachter, Springer-Verlag, 2005.
This conference paper was presented by Andrew Finney at the Computational Methods in Systems Biology 2004 conference held in Paris, May 2004. It discusses early efforts to develop SBML Level 3.
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
Hucka, Michael, Finney, Andrew, Bornstein, Benjamin J., Keating, Sarah M., Shapiro, Bruce E., Matthews, Joanne, Kovitz, Benjamin L., Schilstra, Maria J., Funahashi, Akira, Doyle, John C., Kitano, Hiroaki
Paper published in IEE Systems Biology, 1(1):41–53.
This paper summarizes SBML and the characteristics of SBML-compatible software tools as of early 2004. The article includes a matrix of capabilities that was the inspiration for the SBML Software Matrix now used on this site to summarizes known SBML-compatible software tools.
Systems Biology Markup Language: Level 2 and Beyond
Finney, Andrew M., and Hucka, Michael
Paper published in Biochemical Society Transactions, 32:1472–1473, 2003.
Short paper from a conference in which Andrew Finney described the initial plans for SBML Level 2.
The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models
Hucka, Michael, Finney, Andrew, Sauro, Herbert M., Bolouri, Hamid, Doyle, John C., Kitano, Hiroaki, Arkin, Adam P., Bornstein, Benjamin J., Bray, Dennis, Cornish-Bowden, Athel, Cuellar, Autumn A., Dronov, Sergey, Gilles, Ernst Dieter, Ginkel, Martin, Gor, Victoria, Goryanin, Igor I., Hedley, Warren J., Hodgman, T. Charles, Hofmeyr, Jan-Hendrik S., Hunter, Peter J., Juty, Nick S., Kasberger, Jay L., Kremling, Andreas, Kummer, Ursula, Le Novère, Nicolas, Loew, Leslie M., Lucio, Daniel, Mendes, Pedro, Minch, Eric, Mjolsness, Eric D., Nakayama, Yoichi, Nelson, Melanie R., Nielsen, Poul F., Sakurada, Takeshi, Schaff, James C., Shapiro, Bruce E., Shimizu, Thomas S., Spence, Hugh D., Stelling, Jörg, Takahashi, Kouichi, Tomita, Masaru, Wagner, John M., Wang, Jian, and the rest of the SBML Forum
Paper published in Bioinformatics, 9(4):524–531, 2003.
Original publication about SBML. It describes SBML Level 1 Version 2.

Applications supporting SBML software infrastructure

A Methodology to Annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language
Roehner N., Myers C.J.
Paper published in ACS Synthetic Biology, DOI: 10.1021/sb400066m, 2013.
JSBML: a flexible Java library for working with SBML
Dräger A., Rodriguez N., Dumousseau M., Dörr A., Wrzodek C., Le Novère N., Zell A., Hucka M.
Paper published in Bioinformatics, 27: 2167-2168, 2011.
Description of the JSBML library, a tool to help support SBML in software tools written in the Java language.
LibSBML: An API Library for SBML
Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M.
Paper published in Bioinformatics, 24: 880-881, 2008.
Description of the libSBML, a C++ library to help support SBML in software tools written in a variety of languages.
SBMLToolbox: an SBML toolbox for MATLAB users
Keating, S. M., Bornstein, B. J., Finney, A., and Hucka M
Paper published in Bioinformatics, 22: 1275-1277, 2006.
Description of the SBMLToolbox, a tool to help use SBML in MatLab.

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