Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

After 5 years, free systems biology markup language has proven popular

02.03.2010
A scientific paper that describes a file format used by scientists to represent models of biological processes has exceeded 500 citations in the ISI Web of Knowledge, an online academic database that documents the impact of scientific publications.
The Systems Biology Markup Language (SBML) is designed to enable the exchange of quantitative models of biochemical networks between different computer software packages, allowing the models to be shared and published in a form other researchers can use in various software environments.

Information standards are needed by the systems biology community to help share, evaluate, and develop models of biological processes. Over the years, many scientists and computer specialists have contributed their time and expertise to the development of SBML as part of the international consortium known as the SBML Forum. The paper that first described the SBML information standard and which has exceeded the 500-citation milestone appeared in the journal Bioinformatics in 2003 and is entitled "The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models."

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 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 was coming 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, I was fortunate to be the recipient of Japanese Exploratory Research for Advanced Technology (ERATO) funding. ERATO funding is a large-scale, extremely flexible funding that helped me to support the initiative at an early stage, make the initiative happen, and assist in making the project self-sustainable. 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."

Read the original paper:

* 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 JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere 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 J, Wang J (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4): 524-531.
www.ncbi.nlm.nih.gov/pubmed/12611808?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed
_ResultsPanel.Pubmed_RVDocSum&ordinalpos=7
[PMID: 12611808]

Visit the SBML web site at http://sbml.org/Main_Page

The new SBML Level 3 Core specification is described in the following publication: Hucka, Michael, Bergmann, Frank, Hoops, Stefan, Keating, Sarah, Sahle, Sven, and Wilkinson, Darren. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 1 Candidate). Available from Nature Precedings
http://dx.doi.org/10.1038/npre.2010.4123.1 (2010)

Barry Whyte | EurekAlert!
Further information:
http://www.vbi.vt.edu

More articles from Life Sciences:

nachricht The balancing act: An enzyme that links endocytosis to membrane recycling
07.12.2016 | National Centre for Biological Sciences

nachricht Transforming plant cells from generalists to specialists
07.12.2016 | Duke University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Significantly more productivity in USP lasers

In recent years, lasers with ultrashort pulses (USP) down to the femtosecond range have become established on an industrial scale. They could advance some applications with the much-lauded “cold ablation” – if that meant they would then achieve more throughput. A new generation of process engineering that will address this issue in particular will be discussed at the “4th UKP Workshop – Ultrafast Laser Technology” in April 2017.

Even back in the 1990s, scientists were comparing materials processing with nanosecond, picosecond and femtosesecond pulses. The result was surprising:...

Im Focus: Shape matters when light meets atom

Mapping the interaction of a single atom with a single photon may inform design of quantum devices

Have you ever wondered how you see the world? Vision is about photons of light, which are packets of energy, interacting with the atoms or molecules in what...

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

Im Focus: MADMAX: Max Planck Institute for Physics takes up axion research

The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.

The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

NTU scientists build new ultrasound device using 3-D printing technology

07.12.2016 | Health and Medicine

The balancing act: An enzyme that links endocytosis to membrane recycling

07.12.2016 | Life Sciences

How to turn white fat brown

07.12.2016 | Health and Medicine

VideoLinks
B2B-VideoLinks
More VideoLinks >>>