NIAID awards $18 million contract for biomedical databaseBy Steve Koppes
A computer database designed to help biomedical scientists identify and exploit the weak spots in scores of deadly microorganisms will be established with an $18 million contract from the NIAID (National Institute of Allergy and Infectious Diseases).
Overseeing the effort will be the Computation Institute, a joint effort between the University and Argonne National Laboratory, and the Fellowship for Interpretation of Genomes, a not-for-profit organization specializing in bioinformatics tool development and comparative genomics research.
They will use the funds to set up a National Microbial Pathogen Data Resource Center to help scientists accelerate their research into the biology and evolution of deadly microorganisms and to develop methods for their control.
The new center will provide infectious disease researchers a single Web-based entry point to all relevant organism-related data necessary for their advanced research. The genomes (genetic maps) of hundreds and eventually thousands of microorganisms will be available for integrated analysis.
“The center will directly support the national effort to develop new vaccines, therapeutics and diagnostics for emerging and re-emerging infectious diseases,” said Computation Institute Director Rick Stevens, who will co-direct the center.
“A central goal of the center will be to gather all existing data on these organisms and embed this data within a framework that will support researchers in their efforts to understand them,” said center Co-Director Ross Overbeek.
Working together at the center will be a team of experts in biology, biophysics, microbiology, computer science and bioinformatics (the application of mathematics and computer science to biological problems).
Stevens, a Professor in Computer Science and Director of the Mathematics and Computer Science Division at Argonne, specializes in high-performance computing, collaborative and visualization technologies, and computational science, including computational biology.
Overbeek, a pioneer in the development of comparative genomic databases (PUMA, WIT, ERGO and the SEED), is interested in extracting deeper understanding from analysis of the growing body of genomic data. In 2003, he co-founded the Fellowship for Interpretation of Genomes.
Among the scientists who will directly benefit from the data center will be the eight new Regional Centers of Excellence for Biodefense and Emerging Infectious Diseases that the NIAID of the National Institutes of Health funded last September. The University will operate one of the Regional Centers of Excellence at Argonne National Laboratory. The data center will assist researchers through the application of mathematics and computer science to biological problems.
“Bioinformatics and comparative analysis will drive the rapid advances needed to address the growing body of threats associated with pathogenic microorganisms,” Stevens said. “These advances will occur, however, only in the presence of effective cooperation between experimental research and the bioinformatics efforts.”
To ensure such cooperation, the center’s outreach and training for experimental researchers will be led by the National Center for Supercomputing Applications of the University of Illinois at Urbana-Champaign. “This group has had extensive experience in outreach to researchers in the biological sciences,” Stevens said. Jonathan Silverstein, Director of the Center for Clinical Information at the University, will work with the National Center for Supercomputing Applications to develop outreach for clinical practitioners.
Although the new database will contain numerous genomes, it will focus its work on eight pathogens:
Staphylococcus aureus, which causes a variety of illnesses, including pneumonia and meningitis;
Streptococcus pyogenes, which causes illnesses such as scarlet fever, toxic shock syndrome and necrotizing fasciitis (flesh-eating disease);
Streptococcus pneumonia, which causes pneumonia, meningitis and osteomyelitis, among other maladies;
Vibrio cholerae, the bacterium that causes cholera;
Vibrio parahemolyticus, a bacterium associated with oysters and seafood that causes gastrointestinal illness in humans;
Vibrio vulnificus, another bacterium associated with shellfish and seafood that causes a diarrheal infection;
Listeria monocytogenes, a bacterium that causes listeriasis, an infection that occurs mainly in newborn infants, the elderly and patients with a weakened immune system; and
Campylobacter jejuni, a bacterium that commonly causes diarrhea.