The Canadian effort to decode the SARS (severe acute respiratory syndrome) virus is a veritable showcase of modern-day sequencing and life science computing technology.
The Michael Smith Genome Sciences Centre (GSC) in Vancouver, where the important work was completed early Sunday morning, uses a combination of IBM's biggest commercial servers, Linux workstations, 100-megabit networking, 802.11b wireless and PDAs capable of wireless bar-coding.
On the biology side, the work was done on Applied Biosystems 3730 XL DNA sequencers and MegaBACE DNA analysers from Amersham Biosciences. While neither Amersham nor ABI have yet to crow about their involvement in this landmark work, on Monday IBM offered up an executive for an interview.
"We've been in partnership with them for three years [GSC and its parent, British Columbia Cancer Agency (BCCA)]. We've had our scientists working with their scientists [at IBM] in New York," said Toronto-based Sal Causi, a business executive for IBM Life Sciences.
Causi said the BCCA had almost 400 nodes based on IBM xSeries and pSeries Regatta servers. GSC said it had 90 of those nodes running off eight-way eServers xSeries 440s in a Linux cluster using Beowulf technology. Various nodes are connected via a 100-megabit network over the University of British Columbia's BC Net. The storage capacity for the systems exceeds four terabytes, according to GSC.
"They use [pServer] Regattas as the collection point for data and the xSeries [for the research]," Causi said.
Using this gear, GSC decoded the suspected SARS virus in less than a week, making good on its mission statement.
"The priority of the Centre is to find innovative means to automate the sequencing and fingerprinting process, develop cost-effective measures that will make such research financially viable and utilise state-of-the-art computing facilities to collect, mine, analyse and disperse data collected at this and other genome facilities," reads the second paragraph of GSC's mission statement.
As for cost of the project, a figure is being discussed but has not been made public, according to BCCA spokeswoman Nicole Adams. She said CSG would likely be reimbursed by Genome Canada, the primary funding organ for genomics and proteomics research in Canada.
IBM's xSeries servers are based on Intel's Pentium III Xeon technology. Higher-end models can be upgraded to the Itanium microprocessor. IBM pServers are based on IBM's most powerful microprocessor line, known as the Power architecture.