BLACKSBURG, Va., Jul. 30, 2003– Virginia Bioinformatics Institute (VBI) at Virginia Tech held the first Systems Biology Markup Language (SBML) “Hackathon” on July 29 and 30. Organized by VBI’s Biochemical Networks Modeling Group and sponsored by Sun Microsystems, the event provided a forum for systems biology software developers to exchange ideas and software.
SBML, an XML standard, allows life scientists to exchange biological models, as well as study these models with several different software applications. A few biochemical simulators are already able to exchange models through SBML, among these the popular Gepasi (http://www.gepasi.org/) developed by VBI’s Pedro Mendes.
The Hackathon brought together a group of bioinformaticians who will continue to work together to enable other applications to “talk” SBML. This will help the wider research community by making available better research software. Hackathons are events where programmers meet to develop common software libraries that are later used to enhance several software applications. This hackathon was an excellent means for rapid resolution of SBML-related coding problems. The resulting higher-quality SBML-enabled software will allow life scientists to create sophisticated research models.
The Biochemical Networks Modeling Group at VBI is engaged in several research projects aimed at increasing our understanding of how cells work at the biochemical level using computer programs that simulate the dynamics of biochemical systems. This group is working to integrate knowledge obtained at different levels and produce predictive life sciences models. The group is developing the COPASI software, a successor of the Gepasi simulator, both making use of the SBML standard.
VBI was deemed a “Sun Center of Excellence” (COE) by Sun Microsystems in March 2001. This award resulted from VBI’s cutting-edge research programs and vision for the future. During the three-year partnership, VBI has received over $1 million in computational resources and support for research. In addition, the institute will continue using these resources to further the development of computer-aided research tools. Sun Microsystems sponsored this SBML Hackathon event. SBML For more information, please contact Dr. Stefan Hoops, Dr. Pedro Mendes, or Dr. Susan Faulkner.
July 29, 2003