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DAILY NEWS AND INFORMATION
FOR THE GLOBAL GRID COMMUNITY /
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Applications:
TELESCIENCE FACILITATES BIOMEDICAL
RESEARCH ON GLOBAL GRID
The United States has not placed a high voltage electron microscope in
service
for biomedical research since the 1970s, yet access to these microscopes is
vital for the study of disorders such as Alzheimer's and Parkinson's disease,
as well as mental retardation. To offset this obstacle, and improve speed and
accessibility to microscopic data, the National Center for Microscopy and
Imaging Research (NCMIR), in collaboration with the National Partnership for
Advanced Computational Infrastructure (NPACI), developed Telescience, a
process that provides, through one Web interface, a suite of tools for
end-to-end electron tomography including remote microscopy, bioinformatics,
distributed computing and collaborative visualization. Telescience allows
researchers to access rare, high energy electron microscopes.
Recently, a team of Telescience researchers competed in the annual
Bandwidth
Challenge at Supercomputing 2003, a showcase contest designed to highlight
emerging applications that use significant bandwidth. The team was recognized
with the "Best Application" award for their advanced, real-world use of
computer networks and infrastructure to facilitate international biomedical
research.
The team, representing NCMIR, NPACI, the Biomedical Informatics Research
Network, OptIPuter, and Pacific Rim Applications and Grid Middleware Assembly
programs, assembled a view into their production cyberinfrastructure that
showcased an international consortium of users and a globally-distributed pool
of integrated, heterogeneous resources. They demonstrated specific elements of
the overall Telescience infrastructure, including the ability to query
distributed, federated databases, and transparently initiate secure data
transfers over native IPv6 networks using Grid middleware such as IPv6 enabled
GridFTP. The ability to remotely control and acquire data from remote
instruments was also featured.
In a real-world example of this multidisciplinary approach, collaborators
in
Sweden, Argentina, San Diego and the Supercomputing conference floor were able
to interactively control high performance instruments in Osaka, Japan, and San
Diego. For each control scenario, digital video over IPv6 functioned as an
interactive mechanism for improved multi-scale specimen navigation and
feedback. For remote control of the world's largest electron microscope in
Osaka, Japan, the team demonstrated the use of high definition television over
IPv6, featuring a state-of-the-art HDTV encoding/decoding system developed by
KDDI R&D Labs in Japan, that utilizes the JPEG2000 compression standard.
Through the Telescience Portal, Dr. Héctor Coirini and his group from the
Universidad de Buenos Aires, Argentina, collaborated with researchers in
Stockholm, Sweden to control the Intermediate Voltage Electron Microscope
(IVEM 4000) in San Diego. According to Coirini, "Telescience is providing
Web-based access to specialized instruments that are not otherwise available
to the Argentinean research community. This demonstrates a practical system
for biologists that illustrates how networking can be used effectively to
enable collaborative research on a global scale."
Also featured were two examples of high resolution visualization
applications,
running on a 27 million pixel display wall powered by a Rocks cluster. This
component illustrated the use of high bandwidth networking for parallel
distributed rendering to enable users to interactively manipulate
multi-gigabyte biomedical datasets.
Telescience was the only entry to utilize IPv6 protocols, and showcased a
system where the entire international infrastructure was IPv6 compliant. The
group successfully transferred more than 1Gbit/second over native IPv6
networks, more than has ever been achieved using IPv6 networks in the history
of the Bandwidth Challenge. Participants included the University of
California-San Diego, the San Diego Supercomputer Center, the Universidad de
Buenos Aires, the Karolinska Institute in Sweden, the Cybermedia Center at
Osaka University, the Center for Ultra High Voltage Microscopy in Osaka,
Japan, Taiwan's National Center for High-Performance Computing, Japan, and
KDDI R&D Labs, Japan.
According to Dr. Mark Ellisman, director of the National Center for
Microscopy
and Imaging Research, "Telescience allows international biomedical research
through multiple scales and modalities. We are pleased that the Telescience
team was able to demonstrate and continue to drive the evolution of the United
State's IPv6 infrastructure."
Telescience has created a paradigm shift in the way microscopy is
performed.
Scientists who once had to travel to gather data are now able to access to a
growing number of tools over the Internet to help in the study of
schizophrenia and Alzheimer's disease. Telescience is creating a vision of
biological research in which global collaborations can effectively improve the
evolution of health care.
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