March 18, 2016
Canadian Bioinformatics Workshop Series continues to bridge the gap between computer science and biology
The Canadian Bioinformatics Workshop Series (CBW) was established by Francis Ouellette in 1999 to address the growing need for a workforce knowledgeable in the field of bioinformatics. The series has been an incredible success. Last year there were nine CBW workshops held in Toronto, Montreal and Vancouver, which trained 199 scientists, bringing the total to over 2,000 scientists trained since the series’ start.
We sat down with Michelle Brazas, Manager, Research and Knowledge Exchange at OICR and Manager of Bioinformatics.ca to discuss why bioinformatics training is so important today and where the workshops are headed in 2015.
Q: The field of bioinformatics has changed radically since the series was launched in 1999. How has CBW adapted to this rapid growth?
A: The initial workshops were an introduction to various topics within bioinformatics, which was a relatively new field at the time. There were no undergraduate or graduate programs in the country and very few courses in bioinformatics. So the idea was to offer workshops to give a broad overview into bioinformatics, genomics and proteomics. Today, you can take undergrad courses that give you this broad introduction, so such introductory workshops are no longer needed. In parallel, research technology platforms have changed as well, outputting increasingly larger amounts of data. CBW has mirrored this change, providing advanced topic workshops that address these new technologies and data sets.
Q: Who participates in CBW’s workshops?
A: The predominant group is post-graduate researchers – M.Sc., PhD students and postdoctoral fellows, right through to principal investigators and directors of research. These researchers take the courses to gain the skills to be able to do cursory analyses themselves and to dig deeper into their data or to gain the language to communicate with a professional bioinformatician. But there are also computational biologists and bioinformaticians who take the courses, because they are looking to gain biological insight and an understanding of the larger process of data analysis, as well as to gain the language to talk to researchers they are working with. Bioinformatics bridges pure biology and pure computational science allowing the two to better communicate and do better research together.
Bioinformatics bridges pure biology and pure computational science allowing the two to better communicate and do better research together
Q: Why is there still such a strong need for bioinformatics training?
A: I don’t think there is currently a research domain in the life or health sciences that doesn’t involve bioinformatics. Having some bioinformatics skills allows you to better interrogate and analyze your data. Given that many experiments today produce such a large volume of data, bioinformatics skills allow you to either analyze it yourself or communicate with somebody who is analyzing it – either way if you’re more knowledgeable in bioinformatics you can be more involved in the analysis. With bioinformatics knowledge and skills, you can also integrate more data sets, ask deeper, more integrative questions and ask smarter research questions.
Q: What have been the biggest successes for the CBW so far?
A: CBW has been successful in numerous ways. Firstly, I think we’ve been successful in delivering targeted workshops that provide bioinformatics skills to address data analysis challenges experienced by these new high-throughput technologies and data sets. Our hands-on workshops focus on a data set and work through an analysis pipeline allowing you to gain relevant and applicable skills. I think we’ve also been successful in making our workshops accessible to all Canadian researchers by facilitating registration and travel for students who live outside the cities where we offer courses. Posting our workshop content freely online after a workshop has also helped bring bioinformatics training to anyone who needs it.
We also try to keep pace with the new research and computational technologies (such as working in the cloud environment), data sets and research challenges by growing the number of workshops since 2008 to about 11 workshops per year. And we’ve filled each of the workshops to capacity. Participating in a workshop is only good if you actually learn and retain the skills taught. Here too, we have put effort into ensuring skill retention by demonstrating a skill and then reiterating that skill with assignments, and in some cases allowing the student to compute on their own dataset. Thus participants can follow along and directly apply the skills they are learning to their own research work.
A recent survey to gauge the impact of our workshops on research indicated that CBW has had influence on research direction, scientific publications, as well as collaborations, and even helped in establishing careers. The result is that CBW has established itself as a very strong brand for offering high quality workshops for scientists. Our brand is even gaining international recognition, as we were recently approached to offer our workshops in collaboration with Cold Spring Harbor and the New York Genome Center in New York in 2015.
Q: What are the next steps for CBW?
A: Certainly the collaboration with Cold Spring Harbor and the New York Genome Center is a big step for 2015. Overall, CBW will focus on continued development of workshops in new topics that address research needs. For example, in 2015 we are offering a new workshop in metagenomics [the analysis of microbial communities, or “microbiomes”] which has become an important new research area with potential relevance in many domains including cancer. To prevent research from stalling, we must anticipate what’s next and not just respond to problems researchers are facing.
I also think there could be better synergy with genome centres in Canada to promote workshops and ensure participants from all over Canada have better access to the workshops. I think we need to work on building these relationships to ensure bioinformatics training becomes entrenched in one’s research training. To this end, we are working on better integrating with a Genome Canada Bioinformatics platform application currently under review.
Q: Do you ever see a day when the type of training CBW offers won’t be needed?
A: Bioinformatics is not a field that is going to go away. It’s a necessary component of research today. In my own research career I have witnessed the shift, particularly in high-throughput technology dependent research facilities, from being heavily wet lab-oriented personnel to being heavily informatics personnel. Since bioinformatics tools and databases are constantly evolving alongside new technologies and research, bioinformatics training will continue to play an important role in ensuring researchers have the skills they need.
More information about the Canadian Bioinformatics Workshop series can be found at www.bioinformatics.ca
This interview has been edited for clarity and length.