SRI International Applies Artificial Intelligence Expertise to Advance Systems Biology Research.Business Editors/High-Tech Writers MENLO PARK Menlo Park. 1 Residential city (1990 pop. 28,040), San Mateo co., W Calif.; inc. 1874. Electronic equipment and aerospace products are manufactured in the city. Menlo College and a Stanford Univ. research institute are there. 2 Uninc. , Calif.--(BUSINESS WIRE)--Sept. 13, 2001 Detailed in the Sept. 14th, 2001 Edition of Science Magazine, AI-Based Methods Promise to Speed Collaboration and Progress Within Life Sciences SRI International (company) SRI International - One of the world's largest contract research firms. Founded in 1946 in conjuction with Stanford University as the Stanford Research Institute, they later became fully independent and were incorporated as a non-profit organisation under U.S. , a leading research institute based in Silicon Valley, has developed a novel software system that uses artificial intelligence and symbolic computing Symbolic computing The process of manipulating numbers and variables according to the rules of mathematical logic. Variables are used to represent a real number or a set of real numbers to exact precision. to better understand and manipulate the overwhelming information produced by genome data. SRI's software, Pathway Tools, encodes large and complex scientific theories that are the basis of systems biology Systems biology, a field of study in the biosciences, focuses on the systematic study of complex interactions in biological systems. Particularly from 2000 onwards, the term is used widely in the biosciences, and in a variety of contexts. , leading to a greater understanding of biological systems, improved scientific collaboration, and more rapid integration of disparate sources of bioscience knowledge. Pathway Tools is a software environment that supports query, analysis, and visualization operations for pathway/genome databases. Systems biology studies the complex interactions between all levels of biological information -- genomic DNA genomic DNA n. The full complement of DNA contained in the genome of a cell or organism. , informational pathways, and informational networks -- to understand how they work together. The Pathway Tools form the basis of the EcoCyc(TM) Project (http://www.ecocyc.org/), a symbolic pathway database that describes the metabolic, transport, and genetic-regulatory networks of Escherichia coli Escherichia coli (ĕsh'ərĭk`ēə kō`lī), common bacterium that normally inhabits the intestinal tracts of humans and animals, but can cause infection in other parts of the body, especially the urinary tract. (E. coli E. coli: see Escherichia coli. E. coli in full Escherichia coli Species of bacterium that inhabits the stomach and intestines. E. coli can be transmitted by water, milk, food, or flies and other insects. ), a bacterium studied extensively worldwide because of its role in disease and usefulness in biotechnology. Pathway databases describe biochemical pathways and their component reactions, enzymes, and substrates. Science Magazine Details AI-Based Advancements in Systems Biology A study outlining the role of pathway databases in systems biology research will be published in the September 14, 2001 issue of Science magazine. The study emphasizes the need for artificial intelligence to construct and manipulate systems biology theories, which are growing too large and complex to be grasped by the mind of a single scientist. Encoding the theories in this manner allows computers to verify a theory's internal consistency In statistics and research, internal consistency is a measure based on the correlations between different items on the same test (or the same subscale on a larger test). It measures whether several items that propose to measure the same general construct produce similar scores. , its global properties, and its consistency with external data. This holds a tremendous advantage over conventional approaches, which typically take the form of text-based repositories of theories that lack the means to facilitate computer-based reasoning. "The EcoCyc database is the largest and most detailed theory encoded within the Pathway Tools to date. It integrates information about the bacterium E. coli in one place -- in a computable symbolic form -- allowing us to visualize the largest known genetic network of any organism," explained Dr. Peter Karp, Director of SRI International's Bioinformatics Research Group. "We can now begin to use that network to help interpret the huge volumes of gene expression data being generated by gene-chip experiments." Pathway Databases Enable Bioinformatic Collaboration Although biologists had determined approximately 25 percent of E. coli's genetic network prior to the EcoCyc project, this information was spread across hundreds of articles in different scientific journals. A symbolic database such as the one used in the EcoCyc project allows scientists working in different physical locations to integrate their findings within an interactive, searchable database Refers to databases on the Web that are searchable by typing in a query. The term is quite redundant because all databases are searchable. In fact, that is one of their major features. , enabling the scientific community to have a computational theory for the full system. Completing organisms' DNA sequences (such as human and E. coli) has effectively determined their molecular blueprints. Systems biology seeks to define the interactions among these parts and the manner in which those interactions yield system-wide behaviors of the organism. For this reason, Pathway Tools is being applied to a number of other organisms at SRI and by other researchers. For nearly a decade, the EcoCyc project has been funded by the National Center for Research Resources The National Center for Research Resources or NCRR, is a United States government agency. NCRR provides funding to laboratory scientists and researchers for facilities and tools in the goal of curing and treating diseases. (NCRR NCRR National Center for Research Resources NCRR North Carolina Railroad NCRR Nikkei for Civil Rights & Redress NCRR Network Cost Reduction Ratio NCRR Non Conformance Release Report ), a component of the National Institutes of Health. "This database will provide biomedical bi·o·med·i·cal adj. 1. Of or relating to biomedicine. 2. Of, relating to, or involving biological, medical, and physical sciences. investigators nationwide with a valuable, cost-effective tool that has great potential for unlocking the secrets of pathogenicity of E. coli and a number of other disease-causing microorganisms," said Dr. Michael Chang of the NCRR Comparative Medicine Division. "When many researchers have access to a shared national resource such as this encyclopedia database, not only is the effectiveness of the resource maximized relative to its cost, but the scientific impact is greatly increased. EcoCyc is a unique and powerful resource that will increase our understanding of metabolic pathways and will greatly aid drug research and development." Dr. Karp presented the results of the NIH-supported research at last week's Genomes to Life conference in Washington, D.C., sponsored by the Department of Energy. Acknowledgments Collaborators on the EcoCyc project include: Dr. Julio Collado-Vides, Centro de Investigacion Sobre Fijacion de Nitrogeno, Universidad Nacional Autonoma de Mexico; Dr. Ian Paulsen, The Institute for Genomic Research; Dr. Monica Riley, Marine Biological Laboratory The Marine Biological Laboratory (MBL) is an international center for research and education in biology and ecology. Founded in 1888, the MBL is the oldest independent marine laboratory in the Americas, taking advantage of a coastal setting in the Cape Cod village of Woods Hole, ; and Dr. Milton Saier, Department of Biology, University of California The University of California has a combined student body of more than 191,000 students, over 1,340,000 living alumni, and a combined systemwide and campus endowment of just over $7.3 billion (8th largest in the United States). San Diego. About SRI's Artificial Intelligence Center SRI International's Artificial Intelligence Center is a pioneer and major contributor to the development of computer capabilities for intelligent behavior in complex situations. The Center's objectives are to understand the computational principles underlying intelligence in humans and machines and to develop methods for building computer-based systems to solve problems, to communicate with people, and to perceive and interact with the physical world. About SRI International Silicon Valley-based SRI International (www.sri.com) is one of the world's leading independent research and technology development organizations. Founded in 1946 as Stanford Research Institute Stanford Research Institute - Former name of SRI International. , SRI has been meeting the strategic needs of global markets for 55 years. As part of its strategy to bring its technologies to the marketplace, SRI licenses its technologies, forms strategic partnerships and creates spin-off companies. Note to Editors: SRI International is a registered trademark and EcoCyc is a trademark of SRI International. |
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