Blacksburg, VA, USA. Significant advances in modeling biological processes in recent years are due in large measure to successful deployment of the Systems Biology Markup Language (SBML). The tool is suitable for models of metabolism, cell signaling, and other processes.

SBML supports exchange of quantitative models of biochemical networks between different computer systems, allowing model sharing and publication in a form other researchers can use in their own environments. The initial paper has exceeded 500 citations in the ISI Web of Knowledge, a database that documents the impact of scientific publications. [C1]

The Systems Biology Graphical Notation (SBGN), described in a previous TS-Si.org article, provided a set of standards for graphically representing biological information — the biology equivalent of a circuit diagram in electronics. [C2] The potential convergence with SBML has already demonstrated powerful results and offers the basis for extensions into new realms of research.

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Michael Hucka, a Senior Research Fellow at the California Institute of Technology (Caltech) in Pasadena, and first author of the paper, has chaired the SBML Editors and SBML Team by community consensus since 2003. Today he works on all aspects of SBML and is involved with BioModels.net and consortium efforts such as the BioModels Database.

Said Hucka, "We're all really pleased by this outcome. The number of citations for our original paper is a validation of the usefulness of the SBML language to the scientific community."

"The development of SBML continues at pace thanks to the efforts of both a team of dedicated developers and an international community of volunteers and researchers, who act as SBML users and fellow developers. SBML is a free and open community resource that extends beyond the interests of any single group of researchers."

Back in 1999, when the SBML team came together, some of the early members of the group included Hamid Bolouri, John Doyle, Andrew Finney, Hiroaki Kitano, Herbert Sauro, and Hucka. Hiroaki Kitano, the principal investigator who started the SBML project, is director of Sony Computer Science Laboratories, Inc., and director of the Systems Biology Institute in Tokyo, Japan.

Commented Kitano, "Systems biology has triggered a revolution in biology that in time will hugely impact scientific and medical practice."

"The idea of SBML came from the vision that compatibility and interoperability were going to be the issue once systems biology took-off."

"In 1999, the group that eventually became the SBML Team at Caltech and I organized a workshop to discuss issues in software platforms and how to solve them. This is when we decided to initiate the project."

Since then, many people have found value in the project and the community has grown beyond critical mass. At the time, Hiroaki Kitano received Japanese Exploratory Research for Advanced Technology (ERATO) funding. ERATO funding is a large-scale, extremely flexible funding that supported the initiative at an early stage, make the initiative happen, and assist in making the project self-sustainable. Kitano says that "Breaking 500 in the citation index is a sure sign that SBML is coming of age".

SBML is a computer-readable format for describing qualitative and quantitative models of biochemical reaction networks. It can also be used to express gene regulatory networks and other phenomena of interest in systems biology. Stefan Hoops, computational systems biologist at the Virginia Bioinformatics Institute (VBI) at Virginia Tech, served as an SBML Editor for three years. He helped to develop the latest edition of SBML, which is called Level 3, from 2007 until the end of 2009.

Said Hoops, "SBML continues to develop in new directions. For example, the new Level 3 specification will allow a much more detailed description of biological models. As a modular solution, it is also becoming very easy to incorporate SBML into a wide range of software packages."

Pedro Mendes, associate professor at VBI and professor in the School of Computer Science, University of Manchester, England, commented, "The community-led and community-maintained initiative described in this paper set out to address a fundamental need in the systems biology community, namely to develop a computer language that facilitates communication and research for scientists interested in studying biochemical pathways and networks."

"SBML has been a focal point for the computational systems biology community and a catalyst for new developments in this area of research. This citation milestone affirms that SBML is the main standard in the growing field of systems biology."

Citations[C1] 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, and the rest of the SBML Forum: 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 and J. Wang. Bioinformatics 2003; 19(4): 524-531. doi:10.1093/bioinformatics/btg015
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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.

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[C2] Standardized Graphical Notation For Systems Biology. TS-Si News Service. TS-Si.org (12 August 2009). Link.

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