SOURCE: SRI International

March 25, 2008 14:30 ET

SRI International to Highlight Pathway Tools Capabilities at the Molecular Medicine Tri-Conference in San Francisco, March 25 - 28

SRI's Pathway Tools Now an Emerging Standard for Curated Pathway Databases

MENLO PARK, CA--(Marketwire - March 25, 2008) - SRI International, an independent nonprofit research and development organization, announced today that more than 75 research groups are now using its Pathway Tools bioinformatics software to create pathway databases for organisms with sequenced genomes. In addition, more than 1,300 academic and commercial groups have licensed SRI's Pathway Tools software to access existing databases.

"From microbes to mouse, from metabolic engineering to drug discovery, we're seeing strong growth in Pathway Tools usage across the life sciences," said Peter Karp, Ph.D., director of SRI's Bioinformatics Research Group. "Hundreds of pathway databases now share a common schema, which will facilitate data sharing and comparative analyses."

Several of these pathway database efforts will be highlighted at a session at the Molecular Medicine Tri-Conference to be held in San Francisco from March 25-28, 2008. Speakers will describe the development of Pathway Tools based pathway databases for major biomedical model organisms including the baker's yeast Saccharomyces cereivisae, the soil-living amoeba Dictyostelium discoideum, and the laboratory mouse; and for the Euasterid clade of plants that includes tomato, potato, pepper, and coffee.

Dr. Karp will share recent developments in Pathway Tools including:

--  A new genome-scale visualization tool for cellular regulatory networks
--  A tool for predicting chokepoints in metabolic networks that may
    constitute good anti-microbial drug targets
--  New comparative analysis capabilities including a comparative genome
    browser and pathway and transport comparisons
--  An advanced but intuitive method of formulating complex queries to
    pathway databases

The development of SRI's Pathway Tools has been funded by grants from the National Institutes of Health (NIH), including the National Institute of Allergy and Infectious Diseases (NIAID). SRI's Pathway Tools are used by two NIAID Bioinformatics Resource Centers, Pathema and the PathoSystems Resource Integration Center (PATRIC), to analyze the genomes of infectious disease pathogens. Other groups are developing plant pathway databases for the flowering plants Arabidopsis and Medicago, rice, and other plants.

SRI's Pathway Tools software has a range of capabilities, including prediction of metabolic pathways from genome data, visual display of both individual pathways and the entire metabolic network, and connectivity analysis of metabolic networks. It also provides a complete pathway editing and curation environment. Visual representation of the biochemical network of an organism aids the interpretation of large-scale omics datasets.

A recent breakthrough in Pathway Tools is its ability to automatically generate metabolic wall charts from any Pathway Tools database. This advanced layout algorithm allows users to generate organism-specific metabolic charts more detailed and accurate than traditional metabolic charts found in biology labs worldwide. Such charts can be generated for many organisms, including the 370 organisms for which pathway databases have been developed in SRI's BioCyc database collection at As the various databases are updated to reflect evolving knowledge of the metabolism of an organism, SRI's software technology can immediately generate updated charts.

Pathway Tools software is free to academic or non-profit institutions for research use. A fee applies to other forms of use. Pathway Tools will be available for the Apple Macintosh for the first time in April 2008. See for more details and download instructions.

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 60 years. The nonprofit research institute performs client-sponsored 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.

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