Essential publications about SBML

Table of Contents

This page lists published papers and chapters describing SBML, SBML packages, and core SBML-supporting software such as API libraries. Information about associated standards are not included here; please see the COMBINE website and FAIRsharing for information about related standards.

About SBML and SBML packages

The following papers and chapters describe SBML and SBML packages in general terms, and are useful for context and general perspectives about SBML, SBML development, and related COMBINE standards.

SBML Level 3: an extensible format for the exchange and reuse of biological models Sarah M. Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T. Bergmann, Andrew Finney, Colin S. Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S. Malik‐Sheriff, Stuart L. Moodie, Ion I. Moraru, Chris J. Myers, Aurélien Naldi, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Maciej J. Swat, Denis Thieffry, Leandro Watanabe, Darren J. Wilkinson, Michael L. Blinov, Kimberly Begley, James R. Faeder, Harold F. Gómez, Thomas M. Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson L. Lister, Daniel Lucio, Eric Mjolsness, Carole J. Proctor, Karthik Raman, Nicolas Rodriguez, Clifford A. Shaffer, Bruce E. Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier‐Schellersheim, Herbert M. Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C. Doyle, Michael Hucka, and SBML Level 3 Community members. Molecular Systems Biology 16(e9110), 2020.Summarizes the development of SBML Level 3.
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2020 Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, and Dagmar Waltemath. Journal of Integrative Bioinformatics 17(2–3), 2020.Introduces a special issue of COMBINE standards, including SBML.
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019 Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson and Dagmar Waltemath. Journal of Integrative Bioinformatics 16(2), 2019.Introduces a special issue of COMBINE standards, including SBML.
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017 Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer and Dagmar Waltemath. Journal of Integrative Bioinformatics 15:1, 2018.Introduces a special issue of COMBINE standards, including SBML.
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016 Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer and Dagmar Waltemath. Journal of Integrative Bioinformatics 13:3, 2017.Introduces a special issue of COMBINE standards, including SBML.
Specifications of Standards in Systems and Synthetic Biology: Status and Developments Falk Schreiber, Gary D. Bader, Martin Golebiewski, Michael Hucka, Benjamin Kormeier, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath and Stephan Weise. Journal of Integrative Bioinformatics 12:2, 2016.Introduces a special issue of COMBINE standards, including SBML.
SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools Chaouiya, C., Berenguier, D., Keating, S. M., Naldi, A., van Iersel, M. P., Rodriguez, N., Dräger, A., Büchel, F., Cokelaer, T., Kowal, B., Wicks, B., Gonçalves, E., Dorier, J., Page, M., Monteiro, P. T., von Kamp, A., Xenarios, I., de Jong, H., Hucka, M., Klamt, S., Thieffry, D., Le Novère, N., Saez-Rodriguez, J., and Helikar, T. BMC Systems Biology 7:135, 2013.Describes SBML ‘qual’, 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, S. M., and Le Novère, N. Chapter in In Silico Systems Biology – Methods in Molecular Biology, vol. 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, A., Hucka, M., Bornstein, B. J., Keating, S. M., Shapiro, B. M., Matthews, J., Kovitz, B. K., Schilstra, M. J., Funahashi, A., Doyle, J. C, and Kitano, H. Chapter 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, R., Rost, U., Sahle, S. and Wegner, K. 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, M., and Finney, A. 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, A. Chapter 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, M., Finney, A., Bornstein, B. J., Keating, S. M., Shapiro, B. E., Matthews, J., Kovitz, B. L., Schilstra, M. J., Funahashi, A, Doyle, J. C., and Kitano, H. IEE Systems Biology, 1(1):41–53, 2004.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, A. M., and Hucka, M. 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. Bioinformatics, 9(4):524–531, 2003.Original publication about SBML. It describes SBML Level 1 Version 2.

About software infrastructure

This section is limited to papers authored by SBML Team members specifically about SBML infrastructure software. Many third-party groups have developed other SBML-compatible software, but these are outside of the scope of this list.

MOCCASIN: converting MATLAB ODE models to SBML Gómez, H. F., Hucka, M. Keating, S. M., Nudelman G., Iber, D., and Sealfon, S. C. . Bioinformatics, 32(12): 1905–1906, 2016.Description of MOCCASIN, a Python-based converter of certain types of MATLAB programs. Does not require MATLAB to run.
JSBML 1.0: providing a smorgasbord of options to encode systems biology models Nicolas Rodriguez, Alex Thomas, Leandro Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Harold F. Gómez, Florian Mittag, Jakob Matthes, Jan Rudolph, Finja Wrzodek, Eugen Netz, Alexander Diamantikos, Johannes Eichner, Roland Keller, Clemens Wrzodek, Sebastian Fröhlich, Nathan E. Lewis, Chris J. Myers, Nicolas Le Novère, Bernhard Ø. Palsson, Michael Hucka, and Andreas Dräger. Bioinformatics, 10.1093/bioinformatics/btv341, 2015.Description of the JSBML library, a tool to help support SBML in software tools written in the Java language.
A Methodology to Annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language Roehner N., Myers C.J. ACS Synthetic Biology, 10.1021/sb400066m, 2013.Description of the JSBML library, a tool to help support SBML in software tools written in the Java language.
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. 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. 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. Bioinformatics, 22(10):1275–1277.Describes SBMLToolbox, a MATLAB toolbox built on top of libSBML. It provides a set of basic functions allowing SBML models to be used in both MATLAB and Octave.

SBML specification documents

The SBML Specifications are documents that exist independently of journal publications. Prior to the year 2015, we had difficulty finding an outlet for publishing the specification documents; however, beginning in 2015, the Journal of Integrative Bioinformatics offered to publish annual special issues developed to specifications in the computational biology/bioinformatics area, and thus recent SBML specifications have been published as journal articles.

SBML Level 3 Package: Distributions, Version 1, Release 1 Smith, L. P., Moodie, Stuart L., Bergmann, Frank T., Gillespie, Colin, Keating, Sarah M., König, M., Myers, Chris J., Swat, Maciek J., Wilkinson, Darren J., and Hucka, M. Journal of Integrative Bioinformatics, 17(2–3), 20200018, 2020.
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2 Hucka, M., Bergmann, F. T., Chaouiya, C., Dräger, A., Hoops, S., Keating, S. M., König, M., Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Sheriff, R., Smith, L. P., Waltemath, D., Wilkinson, D. J., and Zhang, F. Journal of Integrative Bioinformatics, 16(2), 20190021, 2019.
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core Hucka, M., Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Smith, L. P., Waltemath, D., & Wilkinson, D. J. Journal of Integrative Bioinformatics, 15(1), 20170080, 2017.
SBML Level 3 package: Multistate, Multicomponent and Multicompartment Species, Version 1, Release 1 Zhang, F. and Meier-Schellersheim, M. Journal of Integrative Bioinformatics, 15(1), 20170077, 2017.
SBML Level 3 package: Render, Version 1, Release 1 Bergmann, F. T., Keating, S. M., Gauges, R., Sahle, S., and Wengler, K. Journal of Integrative Bioinformatics, 15(1), 20170078, 2017.
SBML Level 3 Package: Flux Balance Constraints version 2 Olivier, B. G. and Bergmann, F. T. Journal of Integrative Bioinformatics, 15(1), 20170082, 2017.
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Hucka, M., Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Smith, L. P., Waltemath, D., and Wilkinson, D. J. Journal of Integrative Bioinformatics, 15(1), 20170081, 2017.
SBML Level 3 package: Groups, Version 1 Release 1 Hucka, M., and Smith, L. P. Journal of Integrative Bioinformatics, 13(3), 8-29, 2017.
SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3 Smith, L. P., Hucka, M., Hoops, S., Finney, A., Ginkel, M., Myers, C. J., Moraru, I., and Liebermeister, W. Journal of Integrative Bioinformatics, 12(2), 603-659, 2016.
SBML Level 3 package: Qualitative Models, Version 1, Release 1 Chaouiya, C., Keating, S. M., Berenguier, D., Naldi, A., Thieffry, D., Iersel, M., Le Novère, N., and Helikar, T. Journal of Integrative Bioinformatics, 12(2), 691-730, 2016.
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core Hucka, M., Bergmann, F. T., Hoops, S., Keating, S. M., Sahle, S., Schaff, J. C., Smith, L. P., and Wilkinson, D. J. Journal of Integrative Bioinformatics, 12(2), 382-549, 2016.
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions Hucka, M., Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Smith, L. P., Waltemath, D., and Wilkinson, D. J. Journal of Integrative Bioinformatics, 12(2), 731-901, 2016.
The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints Olivier, B. G., and Bergmann, F. T. Journal of Integrative Bioinformatics, 12(2), 660-690, 2016.
The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core Gauges, R., Rost, U., Sahle, S., Wengler, K., and Bergmann, F. T. Journal of Integrative Bioinformatics, 12(2), 550-602, 2016.