In the News
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.