By Malorye A. Branca
December 15, 2003 | In the future, doctors will not only write personalized prescriptions tailored to specific genetic defects, but also provide guided tours of those defects. “Right here, where that gene turns way, way up, that’s where the trouble is,” a physician might say, pointing to a spot in a molecular pathway unfolding holographically on the office walls.
That particular scenario is probably a few years, or even decades, away. However, it’s not so farfetched to imagine that scientists will soon be working with 3-D models of cellular pathways and other biological processes.
Christoph Sensen is hoping to be one of the first to do just that. Director of the Sun Center of Excellence for Visual Genomics at the University of Calgary Faculty of Medicine, Sensen already commands the world’s first Java 3-D-enabled CAVE—an immersive visualization environment in which photorealistic images are projected onto the room’s walls. (It’s like the holodeck on Star Trek, Sensen says.) The projection technology comes from Fakespace Systems, the products of which are also used by engineers to collaborate on automotive designs. The CAVE is driven by a Sun Microsystems SunFire 6800 server, and TimeLogic DeCypher boards help speed up database searches.
Another key component is Paracel’s GeneMatcher, which the Sun Center recently upgraded to Version 2. GeneMatcher 2 is optimized for sequence analysis, and lots of it. The new system features 28,800 custom processors strung together on a motherboard. It contains a variety of programs, including BLAST and GeneWise. A built-in Linux cluster handles post-processing of raw search results.
“We get to the level of doing millions of searches per day,” Sensen says. One key to getting value from his system is having tools set up to feed it appropriately. “If you don’t feed the pipeline well, you don’t get much from it.”
With his wish list largely fulfilled, Sensen aims to build 3-D representations of genetic processes in cancer progression. To do this, his group will marry gene-expression data to magnetic resonance-generated images. They’ll map changes in gene expression to the corresponding changes in the tumors. Their hope is to find, for example, the very switchpoints that make cells turn cancerous, resistant to immune attack, and able to travel to distant body parts.
“We are trying to combine gene expression and imaging,” Sensen says. “Besides metabolic pathways, we can also look at structural and housekeeping genes.”
The center chose Paracel’s GeneMatcher 2 for its processing power and convenience, he says. “It’s one rack that outperforms a several-thousand-node Linux cluster and has a single operating system. You lock into one system, and then it does it all for you.”
“I have one system administrator for my entire facility,” Sensen says. That facility supports its own research as well as more than 50 projects across Canada, “from Newfoundland to Victoria.” The projects involve a wide range of species, including cattle and opium poppies, which are grown legally in Canada by only one scientist—a genomic researcher.
University of Calgary’s partners in the GeneMatcher 2 purchase include WestGrid, GenomePrairie, the Alberta Science and Research Authority, and Paracel—the maker of the system. WestGrid is an almost-$50-million project aimed at providing scientists across British Columbia and Alberta with an advanced computing infrastructure.