Bioinformatics speed up protein identification

The scientists at Caprion Pharmaceuticals Inc. want to get a clear picture of what a healthy piece of tissue looks like. But while they’ve managed to peek inside cells, they need help to interpret what they see. They hope that a compute farm, along with their unique CellCarta technology, will help them take our hitherto fuzzy knowledge of cells and put it into focus.

Montreal-based Caprion opened the doors to a new facility and a new way of discovering and understanding proteins on Oct. 18.

“This is like watching the football game from the sidelines rather than a Goodyear Blimp,” said Caprion president and CEO Lloyd M. Segal in an event to kick off the new facility.

With the use of its CellCarta technology, the life sciences research firm, which discovered diagnostic tools for Mad Cow Disease and variant Creutzfeldt-Jacob’s Disease, can look at the organelles, or parts, of a cell. Caprion can then extract proteins from the organelles and break those down further into peptides. It can distinguish one peptide from another by figuring out how quickly the peptide travels from point A to point B using mass spectrometers.

But once the data was collected, it took two weeks to perform an algorithm to understand that data using conventional methods. Now, with the help of the Sun compute farm, Caprion has cut that time down to five minutes.

The compute farm consists of Sun Fire servers linked together by Sun Grid Engine software. Data from the mass spectrometers is assigned to idle processors which perform the algorithm and then store the results in an Oracle database. The floor of the room which houses the servers is raised so that the technicians have easy access to the cabling below. The raised floor also facilitates the cooling system – the room must be kept at a temperature of 18 to 19 degrees Celsius. The air is dragged from the floor up through the system, recaptured and re-cooled. The room, like many of the other research rooms at Caprion’s new facility, is protected from direct sun light, which can effect temperature.

Building the system, which was done with the help of systems integrator CGI wasn’t easy, according to Sun technical regional manager Jean-Fran

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