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Francis Ouellette, Director, CMMT Bioinformatics Core Facility



Co-author, with Andreas Baxevanis, of Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 2nd Edition, published by John Wiley & Sons.


Worked at NCBI before signing on as director of the Bioinformatics Core Facility of the Center for Molecular Medicine & Therapeutics in Vancouver, BC, Canada.


Co-founder of the Canadian Bioinformatics Workshop Series. Recently launched to serve as a resource for the Canadian bioinformatics community.


Enjoys spending time with his wife, Nancy Ryder, and daughter, Maya (pictured above). Also enjoys hiking and sea kayaking.

QHow is the Bioinformatics Core Facility set up within the Center for Molecular Medicine and Therapeutics?

AThe CMMT itself is a research center within the Children’s and Women’s hospital within Vancouver, which is affiliated with the University of British Columbia. I was a happily employed civil servant four years ago and gave a talk in Vancouver and was invited by the director of the institute, Michael Hayden, to consider a position here as director of the bioinformatics core facility and also a principal investigator at the research center. Part of my job is to run this core facility.

Michael also gave me another job, and I’m also director of the bioinformatics core facility for the Canadian Genetic Disease Network. The CGDN is a network of human geneticists across the country. The Canadian Bioinformatics Workshop Series and are basically part of my CGDN job.

QWhat hardware do you have in place at the core facility?

AWe run a mixed environment. We have Solaris boxes, we have IBM boxes, and a lot of Linux boxes. At the core facility our servers are Solaris and AIX and all the workstations are Linux boxes.

NCBI is a Solaris shop, so having been raised there in part, I’m definitely a Solaris user, but I like a mixed environment. Today most molecular biology software runs on either on Solaris or Linux and we’re making it run on AIX as well.

QDo you offer any unique resources through the core facility?

AOne big Canadian product that’s highlighted in our web resources that my group is involved in with my colleague’s [Chris Hogue] group in Toronto is BIND. That’s what we call CanCon — Canadian content.

BIND is a working database at for people to use and submit to and so forth. A number of journals are in the process of setting up their guidelines so that if you’re going to submit interaction data to that journal you have to submit your data to BIND. Genome Research does that already.

QDid the recent formation of the Blueprint non-profit company change your work with the BIND project at all?

AThat’s a third hat. We set up Blueprint to be a receptacle and management body for BIND and other related software and tools. We’ve had some success in getting funds from industry and also the Canadian Institute of Health Research. A number of other grants are in the works right now.

QHow did you begin working with the Canadian Bioinformatics Workshop series?

AThere was a survey of industry people and what they thought was missing in the future and bioinformatics was one of them. It was around the time I was recruited here and we got together a bunch of people to set up a series of one- or two-week workshops that would basically be a crash course on bioinformatics. That kind of thing wasn’t provided at the time at any university or environment.

Last year we offered four different workshops: a two-week general bioinformatics workshop followed by three one-week workshops — one in genomics, one in proteomics, and one in tool development. This year we’re offering two new workshops in addition to those four. One is a two-week workshop on introductory programming for biologists and the second is a two-week workshop for more advanced programmers on how to program using the NCBI toolkit.

QApproximately how many researchers have received bioinformatics training through the workshops so far?

AWe have around 50 students in each workshop and we’ve graduated around 300 so far.

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