Telescience Recognized for Facilitating Biomedical
Research on a Global Network
Telescience participants at Supercomputing
2003 demonstrated remote microscope manipulation,
high bandwidth over the next generation Internet protocol
(IPv6), and Web portal options for collaborative international
research. Telescience won "Best Application" during
the annual Bandwidth Challenge.
Thanks to the emergence of
Telescience
, biomedical researchers can now use computer science
and networking advances to access rare microscopes
and imaging tools through one web portal. Resulting
data analysis aids in the understanding of how changes
in microscopic tissue structure influence such disorders
as Alzheimer's and Parkinson's. Developed
by UCSD's National Center for Microscopy and Imaging
Research (NCMIR), in collaboration with the National
Partnership for Advanced Computational Infrastructure
(
NPACI),
Telescience utilizes an infrastructure that includes
internationally distributed computational resources,
high-bandwidth networks, databases, and visualization
software in a manner that hides its complexity from
the user.
From within the portal, multiple users are
able to take turns manipulating specialized biomedical
instruments such as NCMIR's intermediate voltage
electron microscope (IVEM) 4000. These users then
have access to all of the tools and resources necessary
to perform high resolution 3D reconstruction
using electron tomography. The tomography allows researchers
to combine 2D sample images, taken at
specific degrees of rotation, to create the biologically
correct three-dimensional image that includes all
internal substructures. The tomograms allow researchers
to gain a true perspective of the size and structural
complexity of biological systems.
For researchers to capture and review the
image data created through the Telescience Portal
tools, significant bandwidth must be available. Recently,
a team of Telescience researchers competed in the
annual Bandwidth Challenge at Supercomputing 2003,
a 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 (
BIRN),
OptIPuter,
and Pacific Rim Applications and Grid Middleware Assembly
(
PRAGMA)
programs, assembled a view into their production cyberinfrastructure
that showcased an international consortium of users
and a globally distributed pool of integrated, heterogeneous
resources. Multiple international
participants accessed multiple microscopes, and were
able to query their image data securely for biological
information through distributed, federated databases.
Transparently initiated secure data transfers over
native Internet Protocol version 6 (IPv6) networks
using Grid middleware such as IPv6 enabled GridFTP.
IPv6 is the evolving worldwide protocol for Internet
use.
In a real-world example of this multidisciplinary
approach, collaborators in Sweden, Argentina, San
Diego, and the Supercomputing conference floor were
able to control interactively 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 (HDTV) over
IPv6, featuring a state-of-the-art HDTV encoding/decoding
system developed by KDDI R&D Labs in Japan, which utilizes
the JPEG2000 compression standard.
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 manipulate interactively multi-gigabyte biomedical
datasets.
Telescience, the only entry to utilize IPv6 protocols,
featured a system where the entire international
infrastructure was IPv6 compliant. The group successfully
transferred more than one 1 Gb/s over
native IPv6 networks, more than has ever been achieved
using IPv6 networks in the history of the Bandwidth
Challenge. Participants included UCSD, the San Diego Supercomputer
Center (SDSC), 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 (NCHC), Japan, and
KDDI R&D Labs, Japan.
According to NCMIR Director Dr. Mark Ellisman, “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.