Telescience recognized for facilitating biomedical research on a global network

December 09, 2003

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 (https://telescience.ucsd.edu), 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 (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. 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 (HDTV) 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 Dr. 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 (http://www.rocksclusters.org). 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 (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 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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Image available of beautiful brain slice image spanning triple monitors.

University of California - San Diego

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