Joining the genomics community was virtually preordained for Stephen Montgomery. During his undergraduate work at the University of British Columbia in electrical engineering, math, and physics, he had to undergo a defense department background check. The result: "This person said that I would always be interested in ... new things and I could never stay in a dormant area for a long time," Montgomery says. He first came in contact with genomics and bioinformatics work through the British Columbia Cancer Research Centre, and with the rate at which the field moves, he says, "it was a natural fit for me."
Now a PhD graduate student at Canada’s Michael Smith Genome Sciences Centre under supervisor Steven Jones, Montgomery is part of a team funded by Genome British Columbia aiming to improve bioinformatics tools used for applications such as gene regulation and motif scanning. For the past two years, his role as lead for technical software architecture puts him in the position of trying to integrate as many steps as possible "to make a tool that’s very easy for bioinformaticists ... to do the biology," he says. That involves merging a 3D visualization tool, huge amounts of genomic data, and downstream components like PCR primer construction.
The goal is to make everything customizable, down to the way genes and exons are represented, he adds. The all-in-one tool would enable biologists to "look at their genes, do cross-species comparisons, [study] transcription factors and binding sites, build PCR primers off the regions of interest, and take them back to the lab and test them," he says.
A driving force in Montgomery’s program is the push to get all of these tools Web-ready in what he envisions as a peer-to-peer bioinformatics service. "It’s the same way Kazaa works," he says, "but we do it with bioinformatics programs." Users connected to the peer-to-peer network would make their algorithms available and be able to grab ones they need from other users. "We’d like a large number of people to contribute their algorithms [to give] users the best range of choices," he adds.
Montgomery’s group is actively seeking collaborators to help try out these concepts as the software is designed.
— Meredith Salisbury