University of Alberta puts supercomputer to work on Project Cybercell

IBM has donated a supercomputer to the University of Alberta which will be used to improve the way in which researchers can model human cells.

The IBM eServer pSeries 690 supercomputer, worth $1.2 million, will be used principally for the Institute for Biomolecular Design’s Project Cybercell, led by U of A biochemistry professor Mike Ellison.

Ellison said his department is already capable of modelling all two million of the biochemicals that make up a cell, but the issue before them is more a matter of longevity than complexity. Under current conditions, the model may hold up for a fraction of a second, but the goal is to sustain it for hours and days. That goal may be up to five years away, even with the introduction of this latest supercomputer, but the implications are staggering.

“The further we can get, the more relevant and applicable this simulation strategy becomes in the life sciences,” he said. “If you can simulate cellular life, you can start to do real genetic engineering.”

Project Cybercell will encompass genomics, proteomics and metabolomics. For example, it may be possible to establish cell blueprints for manufacture by modeling them first, he said. The completed cells could then be used in medicine or to manipulate matter at the genetic level. There are ethical considerations to all medical research, said Ellison, but the fact that the models can be tested rather than actual cells could be a ethical boon in itself.

Ellison compared the modeling process behind the cell to a CAD program that would be used for automotive engineering – “to be able to design and optimize the simple cell as a machine either as a pharmaceutical dispenser or to be able to use it to produce bio-products,” he said. “That’s the long-term goal of this work.”

The supercomputer will become part of IBM Alberta Centre for Advanced Studies, which opened at the U of A last year. There are 16 such centres around the world, four of them in Canada, with another five on the way.

Ellison praised IBM for its commitment to the university, calling Big Blue “one of the few companies that has made a major commitment to long-term academic research. You’re certainly not going to get this from Sun (or) SGI.”

Rolf Sherlock, executive director for the IBM Alberta Centre for Advanced Studies, said that the company’s supercomputer donation is also a means to observe how groups of people share technology.

Ellison and his team will be the primary users of the pSeries 690, but other departments at the university will get their turn too.

“I think everybody’s come to realize . . . you can get an awful lot more bang for your buck” by sharing resources, said Sherlock. The organizational behaviour that IBM observes at the CAS could help the company establish best practices for other areas of its business, he said.

Within the U of A, a variety of departments may be able to get some hands-on time with the supercomputer. Ellison said computer science, bio-science, chemistry, and possibly economics and business will all find uses for the supercomputer’s number-crunching prowess.

A goal within the university is to break down barriers between departments and focus on interdisciplinary. “We have these vertical silos and there’s not necessarily a lot of communication,” he said, adding that sharing resources like the supercomputer is one way to encourage co-operation and learning.

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