By
ELLEN GOLDBAUM
Contributing Editor
A $1 million National
Science Foundation infrastructure award to store, manage and analyze complex
scientific data is boosting pioneering research at UB in bioinformatics,
geographic information science and other important research areas.
Nearly $600,000 in
matching funds will be contributed to the project by UB and the Strategically
Targeted Academic Research (STAR) Center for Disease Modeling and Therapy
Discovery, funded by the New York State Office of Science, Technology
and Academic Research.
The highly competitive
grant provides UB with the computational infrastructure necessary to manage,
analyze and visualize large-scale, multidimensional data sets that lie
at the heart of some of the university's most cutting-edge research in
drug design, molecular-structure determination and the understanding of
complex geographic images.
"The timing of our
receiving this grant now from the National Science Foundation is key,"
said Jaylan S. Turkkan, vice president for research.
"In conjunction with
our new Center of Excellence in Bioinformatics, it will ensure that UB
is at the leading edge, not only in high-capacity storage of large datasets
that form the knowledge base for bioinformatics, geographic information
science and other important research areas, but also in developing the
complex software tools that will be needed for understanding and analyzing
the data.
"The combination of
these two events is a one-two punch in terms of leveraging UB for large-scale
center grants from the National Institutes of Health and other federal
agencies," Turkkan added.
The new system will
provide the Department of Computer Science and Engineering with 20 times
the amount of data storage it now has in a centrally managed resource
that will assist affiliated researchers working in the departments of
Geography and Pharmaceutical Sciences, and at Hauptman-Woodward Medical
Research Institute and Roswell Park Cancer Institute (RPCI).
In emerging disciplines,
such as bioinformatics and geographic information science (GIS), the issue
of data storage has shifted dramatically from one easily solved by filing
cabinets and the hard drives of PCs to one that can be solved only by
extremely specialized computer equipment.
"The bottom line is,
if you cannot store the data, you cannot do the research," stated Aidong
Zhang, associate professor of computer science and engineering, and principal
investigator on the grant.
Research projects
that are named on the grant include:
- Determination
of the 3-dimensional structure of proteins (Russ Miller, professor of
computer science and engineering, and director of UB's Center for Computational
Research)
- Metadata and knowledge
extraction, representation and management in geographic information
science (David Mark, professor of geography and director of the UB branch
of the National Center for Geographic Information and Analysis, and
Zhang)
- Gene-expression
data analysis (Robert Straubinger, associate professor of pharmaceutical
sciences; Murali Ramanathan, associate professor of pharmaceutical sciences,
and Norma Nowak, director of the DNA Microarray Facility operated by
RPCI and the School of Medicine and Biomedical Sciences)
- Data visualization
(Ashim Garg, assistant professor of computer science and engineering,
and Raj Acharya, now at Penn State)
- Data management
(Zhang)
By the end of the
five-year grant, UB will have a total of 20 terabytes of computer storage
space. A single terabyte is 1 million megabytes. Twenty terabytes is approximately
the same amount of storage found in 1,000 PCs, although researchers caution
that the new system is far more than just a fantastically large storage
space.
"It's not just this
huge amount of storage. It's high-performance storage that enables large
amounts of data to be moved around and accessed quickly and easily," said
Straubinger.
Zhang pointed out
that in addition, the new system will be extremely reliableanother prerequisite
for storing such vast amounts of data, since losing so much data would
be catastrophic for any research project.
"Data is written in
multiple places in the system, so that a hardware failure won't result
in data loss," she said.
The new infrastructure
also will facilitate the kind of computational research required by these
emerging disciplines.
"In pharmacogenomics,
for example, there is a tremendous need for computational research focused
on analysis of the kinds of data we generate, with the objective of better
understanding the mechanism of drug action or how cells and tissues respond
to drugs," said Straubinger.
Zhang, whose expertise
is in database management and data mining, is working with other UB researchers
to develop just those tools.
Having these machines
on campus, she explained, will enable UB computer scientists to begin
to develop the data analysis and visualization systems that will make
working with such large data sets more efficient.
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