Evolution in Bioinformatics Training Programs

ISMB Stockholm, WEB 09 June 30, 2009

Michelle D. BrazasOntario Institute for Cancer

Research

Some Evolution Trees Look Like This…

Darwin

In Bioinformatics, Trees Looks Like This…

The First Generation of CBW Bioinformatics Workshops

• 1999: Need for trained bioinformatic professionals– Only a few bioinformatics training programs existed

– White paper: Bioinformatics Curriculum Recommendations for Undergraduate, Graduate and Professional programs (2002)

• The Canadian Bioinformatics Workshops (CBW) series was created in 1999

– Scientific Director: Francis Ouellette; Scientific Manager: Stephen Hearst – Core Faculty: Stephen Hearst, David Wishart, Chris Hogue, Francois Major,

Christoph Sensen

Model for 1st Generation Workshops

• Workshops offered in various cities across Canada– Travel to participants to reach widest audience– Fredericton, Ottawa, Montreal, Toronto, Windsor, Calgary, Edmonton, & Vancouver

Model for 1st Generation Workshops

• Workshops offered in various cities across Canada– Travel to participants to reach widest audience– Fredericton, Ottawa, Montreal, Toronto, Windsor, Calgary, Edmonton, & Vancouver

• Class size limited to 50 participants per workshop– Lectures + hands-on labs to gain experience using the tools + marked assignments– Highly interactive courses which included events for participant & faculty networking

Model for 1st Generation Workshops

• Workshops offered in various cities across Canada– Travel to participants to reach widest audience– Fredericton, Ottawa, Montreal, Toronto, Windsor, Calgary, Edmonton, & Vancouver

• Class size limited to 50 participants per workshop– Lectures + hands-on labs to gain experience using the tools + marked assignments– Highly interactive courses which included events for participant & faculty networking

• Taught by faculty prominent in their field– Faculty develop & deliver material– Material reviewed and updated yearly at stakeholder meetings– Assisted by trained teaching assistants

Model for 1st Generation Workshops

• Workshops offered in various cities across Canada– Travel to participants to reach widest audience– Fredericton, Ottawa, Montreal, Toronto, Windsor, Calgary, Edmonton, & Vancouver

• Class size limited to 50 participants per workshop– Lectures + hands-on labs to gain experience using the tools + marked assignments– Highly interactive courses which included events for participant & faculty networking

• Taught by faculty prominent in their field– Faculty develop & deliver material– Material reviewed and updated yearly at stakeholder meetings– Assisted by trained teaching assistants

• Hardware & software provided for participants– Most did not own personal laptops

Model for 1st Generation Workshops

• Introductory courses offered– Introduction to Bioinformatics Workshop (2 weeks)– Genomics Workshop (1 week)– Proteomics Workshop (1 week)– Developing the Tools Workshop (1 week)

• Certificate in Bioinformatics– Required 110 hrs class time:

– Certificate was accredited by University of Toronto, University of New Brunswick, and University of British Columbia since by 2003, still only 14 universities across Canada offered any material in bioinformatics

Bioinformatics (2 weeks)

Genomics (1wk) Proteomics (1wk) Developing the Tools (1wk)

Changing Landscape

• All major institutions have bioinformatics content– Introductory material now offered by universities + colleges

– Degree programs

– Independent courses

– Integration of bioinformatics material in most life science courses

– Other tutorials and online courses in bioinformatics

• Declining interest in 1st generation CBW workshops– Today, students already receive extensive exposure to introductory

bioinformatics material

– CBW saw declining enrolment in 1st generation workshops (2006-2007)

CBW: 1999-2007• 1st generation CBW model was extremely successful

– CBW addressed growing gap in scientific training– CBW filled niche market in new field of bioinformatics– Trained >1000 participants & granted >175 certificates– Participants ranged from graduate students to researchers from academia,

government and industry– Participants were drawn from across Canada, US & international

• Time for re-invention of bioinformatics workshops• Mission and vision of CBW remain

CBW Mission: To accelerate the use of bioinformatics as a tool in health and life sciences through education, networking and outreach

CBW Vision: To become a world leader in bioinformatics education, networking and outreach

CBW: Beyond 2007

Science 319: 1599

And the Bioinformatics Evolution Continues

The Second Generation of CBW Bioinformatics Workshops

• Many advances in genomic & proteomic technologies, resulting in new data and bioinformatics tools– Need for advanced training in these new bioinformatic topics

– Need for ‘continuing education’ style workshops

• New model & new CBW workshops introduced in 2008

• 2-day workshops on advanced bioinformatics topics– Interpretation of Gene Lists from -omics Studies– Informatics on High-Throughput Sequencing Data– Clinical Genomics and Biomarker Discovery– Systems and Network Biology– Essential Statistics in Biology

Model for 2nd Generation Workshops

• Workshops offered in one location– High awareness of bioinformatics need– Participants willing to travel to gain required training

• Taught by faculty prominent in their field– Same high quality instruction

• Class size limited to 30 participants– Same highly interactive formula: lectures + hands-on labs– Additional component: participants are required to bring their own data

• 2-day short course– Addresses time constraints of participants– Knowledgeable participants already experienced with the technology

• Personal laptops– Majority of students possess their own laptops & prefer their own environment

Sample 2nd Generation Workshop:

“Interpreting Gene Lists”Faculty:Faculty: Gary Bader, Quaid Morris and Wyeth Wasserman Gary Bader, Quaid Morris and Wyeth Wasserman

Day 1Day 1• Introduction to gene lists

– Tools: GO Ontology, Cytoscape

• Finding over-represented gene functions– Tools: GSEA, GeneMania

• Lab time: Working with your own data

Day 2Day 2• Predicting transcriptional regulation

– Tools: oPOSSUM, Galaxy

• Pathway and network analysis– Tools: Cytoscape

• Lab time: Working with your own data

New Challenges in Bioinformatics Training

• Computational power required by large data sets and programs is more than the capacity of a personal laptop– High-throughput sequencing data sets are large & computationally

intense

– Cloud computing models or server clusters required

3.2PB storage6,224 cores

New Challenges in Bioinformatics Training

• Participants are unfamiliar with command line– With new datasets & tools, having command line experience is

necessary

• Statistical background is often weak– Compounded by larger and more complex datasets

New Opportunities

• Basics in bioinformatics– Command line familiarity and statistics basics

• Responsive development & delivery of new bioinformatics courses

– New technologies will continue to arise, generating new datasets– To meet the need for bioinformatic training to accompany these advances, new

bioinformatic courses will need to be rapidly generated & delivered

• Techniques in data integration– Future bioinformatic courses will need to teach data integration techniques

rather than just techniques for individual data analysis– E.g. Pathways, Systems Biology, etc.

• Bioinformatics training programs can utilize new communication technologies to reach wider audiences

– Podcasts and other live media streams

CBW Sponsors: Past & Present

CBW Sponsors: Past & Present

U d’O

Many Thanks

• Francis Ouellette• Past & present CBW contributors • Ontario Institute for Cancer Research