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ERATO Funding Ends, but SBML Lives on with Help from Growing Systems Biology Community

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Anyone working in the area of systems biology research will tell you that networks are everything, but it turns out that social networks may be just as important in the field as biological ones: When the Systems Biology Markup Language project faced a funding crunch this past fall, a group of like-minded organizations pitched in financially to keep the project running.

The five-year Kitano Symbiotic Systems Project, led by Sony computer scientist Hiroaki Kitano and supported by a ¥1.7 billion ($16 million) grant from the Japan Science and Technology Agency's ERATO (Exploratory Research for Advanced Technology) program, started in October 1998. When John Doyle’s lab at the California Institute of Technology began work on SBML in mid-2000, Kitano agreed to use a portion of the ERATO grant to support three full-time SBML developers.

Last fall, as an expected NIH grant was delayed and the end of the ERATO funding drew near, rumors began circulating that the SBML project was in danger. But, according to Michael Hucka, a researcher in Doyle’s Control and Dynamical Systems group at Caltech, funding pledges soon began flowing in from several other sources — including the UK’s BBSRC, Japan’s New Energy and Industrial Technology Development Organization, the US Defense Advanced Research Projects Agency’s BioSPICE program, and the Molecular Sciences Institute — to keep SBML afloat.

In addition, SRI International, which currently serves as the systems integrator for the DARPA BioSPICE project, agreed to take over further development and maintenance of the Systems Biology Workbench software package. Hucka said that the Caltech/ERATO group no longer had the resources to continue maintaining the software package in addition to SBML. He added that SRI will continue to maintain SBW as an open source project.

Kitano’s research, meanwhile, will continue under a new, smaller grant from JST’s SORST (Solution Oriented Research for Science and Technology) program. The new project will focus on systems biology related research, and a portion of it will go toward SBML support.

More recently, Doyle’s team was awarded a $285,000 NIH grant to support continued development and support of SBML [see NIH funding roundup, p. 4]. The three-year grant will support Hucka, along with Andrew Finney, an SBML developer at the University of Hertfordshire in the UK, as full-time employees, and “guarantee a certain degree of stability to the effort,” Hucka said. In addition, the Doyle group has received a four-year, $1.3 million NSF Information Technology Research grant [BioInform 12-15-03], which will indirectly support development of SBML.

Currently, Hucka said, in addition to himself and Finney, about six developers work on SBML part-time, and the extended group of “active” developers numbers around 30-40. Interest in the project is growing in step with mounting interest in systems biology research, he said, and a number of commercial software firms have taken steps to add SBML capabilities to their products, including ”two major vendors of mathematical software platforms.”

The team is currently in the planning stages for level 3 of SBML. New features in the works include support for a standardized method of drawing and exchanging biochemical networks and other diagrams, as well as a way to represent complex chemical entities that can exist in multiple states, such as phosphorylated proteins.

This spring, April 30 - May 1, the SBML team will host a hackathon at the European Bioinformatics Institute in Hinxton, UK, where Hucka said the group hopes to take a first crack at some of the new features. More importantly, he said, developers will have a chance to test the interoperability of their own SBML-based software systems. Further information on the hackathon, is at http://sbml.org/index.psp.

— BT

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