Hoops named Systems Biology Markup Language editor

Stefan Hoops, computational systems biologist at the Virginia Bioinformatics Institute (VBI), has been named an SBML (Systems Biology Markup Language) editor by the SBML community. In this position, he will help manage the overall SBML development process, leading to new editions of the language.

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. Since technological advances are contributing to more complex quantitative models, information standards are needed by the systems biology community to help share, evaluate, and develop models cooperatively. SBML is designed to enable the exchange of biochemical network models between different software packages, allowing for the sharing and publishing of models in a form other researchers can use in various software environments.

VBI Associate Professor Pedro Mendes and Hoops have been active members of the SBML community from its beginning in 2000 and organized the first SBML Hackathon, which was held at VBI in July 2003. The COPASI software, which has been developed by Mendes, Hoops and colleagues, in collaboration with Ursula Kummer at EML Research gGmbH in Heidelberg, Germany, supports the SBML standard.

“I congratulate Stefan for this vote of confidence he received from the systems biology community,” Mendes said. “Stefan has been a strong contributor to the SBML specification. In his new role, he will provide leadership in the continuing development of SBML.”

SBML development is directed by the systems biology community and coordinated by the SBML Editors. The editors facilitate the process from proposal to final specification by maintaining the SMBL website, monitoring the discussions, editing the new specification, and organizing the SBML forum meetings, which are annual face-to-face meetings.

Members of the SBML community nominate and vote for those that will serve as SBML Editors. The current number of SBML Editors has been expanded from two to five, each serving a term of three years. Hoops will begin his term on January 1, 2007.

The Virginia Bioinformatics Institute (VBI) at Virginia Tech has a research platform centered on understanding the “disease triangle” of host-pathogen-environment interactions in plants, humans and other animals. By successfully channeling innovation into transdisciplinary approaches that combine information technology and biology, researchers at VBI are addressing some of today’s key challenges in the biomedical, environmental and plant sciences.