SRI International to Expand MetaCyc Metabolic Pathway Database Under New Grant from National Institutes of Health

New Developments Planned to Aid Basic Research and Genome Analysis through Visualization of Metabolic Pathways

MENLO PARK, California – May 17, 2004 – SRI International, an independent research and development organization, announced today that it has received a three-year grant from the National Institute of General Medical Sciences (NIGMS), a component of the National Institutes of Health, to expand development of MetaCyc metabolic pathway database.

MetaCyc is a collaboration between SRI and the Carnegie Institution, Department of Plant Biology. It serves as a read ily accessible source of up-to-date, literature-curated information on metabolic pathways and enzymes. The information is used by researchers for basic research and genome analysis, and by students and teachers for educational purposes. MetaCyc can be used by scientists to visualize metabolic pathways from more than 230 organisms.

Under the grant, SRI and Carnegie will continue to curate MetaCyc and further develop SRI's Pathway Tools software, which is used to query, visualize, and edit MetaCyc.

The grant allows SRI and Carnegie to expand MetaCyc's size and scope, address the wealth of metabolic pathway information available in scientific literature, and continue to serve the growing audience for this information.

The expansion will include these developments:

•  Expansion of database content on pathways and enzymes for microbes and plants, and expansion of chemical compound data

•  Linking MetaCyc to other bioinformatics databases

•  Enhancing the visual displays and internal representations of pathways and chemical compounds, and improve visualization of expression data on pathways

•  Enhancing the Pathway Tools software used to support the querying, visualization, and editing of MetaCyc

One of MetaCyc's primary applications is as a reference database for computationally predicting the metabolic network of an organism from its annotated genome using algorithms pioneered by an SRI team led by Peter Karp, Ph.D., director of SRI's Bioinformatics Program.

Metabolic engineers use MetaCyc as an encyclopedia of metabolic pathways and enzymes that may be genetically engineered into an organism to alter its metabolism. The systems biology community uses MetaCyc in global studies of biochemical networks. MetaCyc data can benefit several scientific disciplines, including genetics, molecular biology, microbiology, biochemistry, genomics, bioinformatics, metabolic engineering, and systems biology.

MetaCyc is available through www.metacyc.org and to the scientific community as a set of flat files and as an application program for Linux/Intel, Windows/Intel, and the Sun workstation.

About MetaCyc and Pathway Tools

MetaCyc is part of SRI's BioCyc Database Collection, a collection of queryable pathway/genome databases that includes EcoCyc, HumanCyc, and databases for 16 other species. The MetaCyc metabolic pathway database contains data from 230 species. Scientists can use BioCyc databases to visualize the layout of genes within a chromosome, a complete biochemical pathway, or the full metabolic map of an organism.

Underlying the BioCyc Database Collection is SRI's Pathway Tools – novel software that combines representation and inference techniques from artificial intelligence with extensive scientific visualization capabilities. The software enables both analysis and web publishing of model-organism databases that integrate genome and pathway information to harness the overwhelming amount of information produced by large-scale genome sequencing efforts.

About SRI International

Silicon Valley-based SRI International is one of the world's leading independent research and technology development organizations. Founded as Stanford Research Institute in 1946, SRI has been meeting the strategic needs of clients for more than 55 years. The nonprofit research institute performs contract research and development for government agencies, commercial businesses and private foundations. In addition to conducting contract R&D, SRI licenses its technologies, forms strategic partnerships and creates spin-off companies.

About Carnegie Institution, Department of Plant Biology

The Carnegie Institution, a private, nonprofit organization engaged in basic research and advanced education in biology, astronomy, and the earth sciences, was founded and endowed by Andrew Carnegie in 1902 and incorporated by an act of Congress in 1904. Andrew Carnegie conceived the Institution's purpose "to encourage, in the broadest and most liberal manner, investigation, research, and discovery, and the application of knowledge to the improvement of mankind." The Department of Plant Biology engages in basic research in modern plant science. Located on the campus of Stanford University and equipped to study plants both in the field and in the laboratory, the Department offers students a unique research environment.

About the National Institute of General Medical Sciences (NIGMS)

NIGMS supports basic biomedical research that lays the foundation for advances in disease diagnosis, treatment, and prevention. The Institute's programs encompass the areas of cell biology and biophysics; genetics and developmental biology; pharmacology, physiology, and biological chemistry; bioinformatics and computational biology; and minority biomedical research and training. NIGMS is part of the National Institutes of Health, U.S. Department of Health and Human Services.

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