IT turning science inside out

“Take them to the CAVE,” intones a voice from the back of the rather ordinary-looking elevator crammed with journalists. The doors open to reveal a dark-veiled room hidden deep within the University of Calgary’s Faculty of Medicine, and what lies beyond the curtains just may hold the answers to some of the world’s great mysteries.

U of C and Sun Microsystems Inc. launched the Sun Center of Excellence for Visual Genomics late last month, a new kind of bioinformatics facility which uses immersive 3D technology to view complex data of the human body.

The centre – to be run by Dr. Christoph Sensen, professor of biochemistry and molecular biology at U of C – has the ability to create 3D models of biological systems such as genomes, organs and cancerous cells, using a technology called CAVE (CAVE Automatic Virtual Environment) from Kitchener, Ont.-based Fakespace Inc.

Often compared to Star Trek‘s famous Holodeck, the CAVE is a large, dark room with 270 degree projection systems, as well as floor projection. People may stand inside, and with the use special 3D glasses and other virtual reality gear, actually feel as if they are part of the environment they are seeing. In fact, the computer-generated models are so life-like, observers often try to reach out and touch them.

Being inside the CAVE is “like climbing inside your TV and playing with all the little people,” Sensen said. The hope for scientists, he said, is to be able to understand complex diseases by visualizing aspects of the human body as a collective, something that researchers are unable to do thoroughly with traditional tools such as MRIs or microscopes. “We’ve never been able to see the overall picture before,” he said.

Dr. Randal Johnston, president and CEO of Genome Prairie, said the centre will help “draw order out of chaos,” because humans are much better at recognizing patterns in three and four dimensions than in one-dimensional data on a screen.

“We will be able to draw out, from those data streams, very subtle signals of information hidden in a vast array of biological noise,” Johnston said.

Sensen also expects this technology to cut down the need for medical experimentation with lab animals and human cadavers because, in many cases, they will be able to duplicate digitally the human body’s reactions to events instead.

Though this centre was created to study genomes, Sensen said the same technology could be applied many other data-intensive industries which require visualization, such as oil and gas, geophysics, construction, automotive design and architecture.

Total investment in the Sun Center of Excellence for Visual Genomics is more than $6 million, and funding partners include Sun Microsystems, Fakespace, Western Economic Diversification Canada, the Alberta Science and Research Authority, the Alberta Network for Proteomics Innovation, Genome Prairie and the University of Calgary.

Stefan Unger, business development manager for computational biology at Sun, said this centre is the first of its kind to use CAVE technology in the bioinformatics space.

“This is a centre in visual genomics…one of the problems that we have is that genomics are entering a phase of exponential, and even super-exponential growth, of the amount of data. And not only just in sheer quantity, but in the complexity of the data. One of the ways of trying to get a hold of this is to try to represent this data in a visual manner,” he said.

Dr. Terry Gaasterland echoed Unger’s explanation of why visualization is important in data-intensive research.

Gaasterland, assistant professor and head of Gaasterland Lab at Rockefeller University in New York, worked with Sensen to develop a system called MAGPIE – a fully automated genome analysis and annotation engine. “This is more than 100 Manhattan phone books (worth) of information. And, the open question that came immediately was: ‘how do we really read this?'”

The centre houses a high-performance Sun Fire 6800 server and Sun Ray thin clients for graduate students to access the computer network. It’s home to about 30TB of storage, an amount expected to double over the next two years, according to Chris Spindler, a technical architect for Sun Canada in Calgary.

He said most other CAVEs in the world are used in areas other than life sciences and run on proprietary software, which makes it more difficult to have a collaborative environment to visualize data. The CAVE at the Calgary centre uses Java 3D technology, allowing scientists an open-source, immersive environment to view 3D models of biological systems, including cells, tissues and entire organisms. This could be instrumental in determining how diseased cells react differently than normal ones, for example. “If you understand how something works, you start to understand how to fix it,” he said. “Once you have [the view] you can digitally inject chemicals into the cell, and see how those chemicals behave. You can cut down (live) experiments from, say, 20 to five.”

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