Sun helps launch medical 'holodeck'

The University of Calgary and Sun Microsystems have launched the Sun Centre of Excellence for Visual Genomics, a new kind of bioinformatics facility which uses 3D technology to view complex data of the human body.

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

Often compared to Star Trek's famous Holodeck, the CAVE is a dark, black-curtained room with 270 degree projection systems, as well as floor projection. People may stand inside, and with the use of special 3D glasses and other virtual reality gear, actually feel as if they are part of the environment they are seeing.

Being inside the CAVE is "like climbing inside your TV and playing with all the little people," according to Sensen. He said the hope is for scientists to be able to understand complex human diseases by visualising aspects of the human body as a collective, something that researchers are unable to do as thoroughly with traditional tools such as MRIs or microscopes.

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.

Total investment in the centre is more than C$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.

The centre includes 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 30T bytes of storage, an amount expected to double over the next two years, according to Chris Spindler, a technical architect for Sun 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 visualise data. The CAVE at the centre uses Java 3D technology, allowing scientists an open-source, immersive environment to view three-dimensional 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," Spindler explained.

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," he said. "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."