Publications
The following are published papers and chapters specifically about SBML, written by members of the SBML Team and/or the SBML Editors. This list is limited to publications about SBML only, and does not include other publications about projects involving the authors, nor projects closely related to SBML (such as SBO, MIRIAM, and others), nor about libSBML or other software accessible from this site. Please see the relevant pages and websites for the projects and software to find other publications.
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.
2006
Finney, Anrew, 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.)
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. This is currently the de facto accepted standard format for storing layout in SBML. 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.2005
Hucka, Michael, and Finney, Andrew
Paper published in Molecular Systems Biology, doi:10.1038/msb4100015, 2005.
This is a 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.
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.
2004
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.
2003
Finney, Andrew M., and Hucka, Michael
Paper published in Biochemical Society Transactions, 32:1472–1473, 2003.
This is a short paper from a conference in which Andrew Finney described the initial plans for SBML Level 2.
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.
This is the original publication about SBML. It describes SBML Level 1 Version 2.