Medical "holodeck" opens in Calgary

CALGARY – A new center of excellence on the bleeding edge of bioinformatics will take on complex genetic diseases with funding and computing power fueled by public and private sector partnerships including Sun Microsystems Inc.

The Sun Center of Excellence in Visual Genomics went live Thursday at the University of Calgary and will benefit students, industry collaborators and scientists studying a broad range of diseases, including cancer, lupus and Alzheimer’s.

Bioinformatics is an emerging research field that organizes and maps the complex information used in life sciences research. Since Celera Genomics announced it had finished sequencing the entire human genome in April, the amount of genomic data available for analysis has grown enough to fill 100 Manhattan phone books, said Terry Gaasterland, assistant professor at The Rockefeller University’s Laboratory for Computational Genomics in New York. “The question becomes, ‘How do we really read this?’”

Hence an important feature of the Sun COE is its fully immersive display environment with four projection walls. This CAVE Automatic Virtual Environment (CAVE), developed by Kitchener, Ont.-based Fakespace Systems, is the first of its kind in the world, claim U of C officials, and will enable scientists and researchers to immerse themselves in 3D models of biological systems, including cells, tissues and entire organisms.

Dr. Christoph Sensen, professor of biochemistry and molecular biology at the U of C, said the facility will help reduce the blood and guts in medical research. For example, students studying the inner year right now would have to have access to a cadaver in order to study it up front. With CAVE, the inner ear could be studied virtually, and just as it would eliminate the need for human cadavers, so would it also reduce the need for lab animals, said Sensen.

“It’s like being inside the TV and playing with the little people,” he said, “(or) being on the holodeck of the Enterprise.”

The CAVE is enabled by Java 3D technology from Sun, which means researchers from across the country and even around the world will be able to access data generated at the COE, and develop CAVE applications on any Java technology-enabled computer.

The COE also includes a high performance Sun Fire 6800 server, Sun Ray thin clients for graduate students to access the computer network, and 30 terabytes of available storage.

“Genomics is entering a stage of exponential growth in data,” said Stefan Unger, business development manager for computational biology at Sun. “This is the first if what we hope will be a series of centers in visual genomics.”

The centre is also the first node of the Canadian Bioinformatics Resource in Alberta, a network linking universities and government research labs across Canada.

Total funding of the COE to date is pegged at more than $6 million from partners including Sun, Fakespace, Western Economic Diversification Canada, the Alberta Science and Research Authority (ASRA), the Alberta Network for Proteomics Innovation, Genome Prairie and the U of C. Other participating universities thus far include the University of Alberta in Edmonton and the University of Lethbridge, which house their own servers and are connected by the province’s high speed network, Supernet.

The U of A has an earlier version of CAVE concept, and Sensen said it is likely it will be upgraded in the near future. There are also already plans in the works for a second CAVE at the U of C campus and he sees a market for three or four in Calgary by the end of this year.

The CAVE could also be used for other applications, said Sensen. “You could recreate a whole crime scene in virtual reality.” It may also be useful to third parties both in life sciences and out, he added. “As long as it’s the only one in Calgary there will be huge pressure to lease it out.”

Sensen himself is a botanist and was wooed to the U of C from Halifax by the Alberta advantage, he says. The Nova Scotia government isn’t proactive enough to develop joint partnerships such as the one funding the Sun COE, which was a quick sell in Alberta. “If you want to do science in Canada, Alberta is the place to do it.”

According to Robert Church, chairman of ASRA, the province is focusing strategically on growing the province’s technology capabilities in three years — information communications technology, energy and life sciences. For its part, the U of C is looking to build on its strengths, said Keith Archer, vice-president of research. “Our goal is to assemble Canada’s leading program in bioinformatics,” he said. “The launch of the Sun Centre of Excellence is a major step forward in achieving that goal.”

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Gary Hilson
Gary Hilson
Gary Hilson is a Toronto-based freelance writer who has written thousands of words for print and pixel in publications across North America. His areas of interest and expertise include software, enterprise and networking technology, memory systems, green energy, sustainable transportation, and research and education. His articles have been published by EE Times, SolarEnergy.Net, Network Computing, InformationWeek, Computing Canada, Computer Dealer News, Toronto Business Times and the Ottawa Citizen, among others.

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