Ouellette elixir 2017
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Reflections on Life Science Data Infrastructures in Canada
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Ouellette elixir 2017
- 1. Reflections on Life Science Data Infrastructures in Canada Rome, March 20, 2017 B.F. Francis Ouellette CSO / VP Scientific Affairs, Génome Québec Montréal, QC, Canada francis@genomequebec.com
- 2. Disclamers • I am an employee of Génome Québec, which is part of the Genome Canada family. • I do not (and will not) profit in any way, shape or form, from any of the brands, products or companies I may mention. • I am a big proponent of Open Access, Open Source, Opent Data and Open Courseware • I am on the SAB of many NIH funded projects (SGD, Galaxy, GenomeSpace, H3ABionet, and HMP2), in addition to Elixir.
- 3. in Memory of Anna Tramontano
- 5. Outline of my Reflections • The Parameters: “Made in Canada” • Building a National Bioinformatics Strategy for Canada • The Cancer Genome Collaboratory • Lessons Learned
- 6. Funding Landscape in Canada • 4.5 time-zones, 35 million people, bilingual country, 10 provinces, 3 territories https://en.wikipedia.org/wiki/Canada • Tri-Council: • CIHR http://www.cihr-irsc.gc.ca/ • NSERC http://www.nserc-crsng.gc.ca/ • SSHERC http://www.sshrc-crsh.gc.ca/ • Genome Canada (GBC-GAlta-GP-OG-GQ-GAtl) https://www.genomecanada.ca/ • CFI / MSI https://www.innovation.ca/awards/major-science-initiatives-fund • Compute Canada https://www.computecanada.ca/ • CANARIE https://www.canarie.ca/language/ • Network Centres of Excellence http://www.nce-rce.gc.ca/ • Many provincial funding bodies, with budgets more or less proportional to their population size.
- 9. … and there is also lots of DATA to integrate • ICGC is in the 10-15 PB scale • Healthcare is as well • Biology is more complex than particle physics
- 10. Why a strategy? • Genome Canada • CIHR • NSERC • SSHRC
- 11. The stakeholders need it • Life scientist and bioinformatics research communities • Public and private funding bodies • Infrastructure providers • HPC • Ultra high-speed digital networks • Alliances working to coordinate research data • the Canadian population
- 12. Why a strategy? • Genome Canada • CIHR • NSERC • SSHRC • CFI • Compute Canada • CANARIE • Universities • Private sector
- 14. 18 years in the making 1999 1st Canadian Bioinformatics Workshop delivered 2000 Genome Canada is created 2001 GC & CIHR host 1st Bioinformatics strategic workshop 2003 completion of 1 human genome project 2011 GC & CIHR host 2nd Bioinformatics strategic workshop 2014 GC & CIHR puts together a strategic plan working group 2016 Strategic plan working group delivers final document 2017 Plan is integrated in some of the partner’s plans, and made public
- 15. small expert steering committee SESC + community workshop SESC + stakeholder workshop Larger community consult SESC + community workshop stakeholder & community consult SESC + community workshop Finished document 2015 SESC + community workshop SESC + writer > Strategic Plan
- 16. Strategic Objective 1: Networking and Coordination
- 17. Networking and Coordination Step 1: Organization a Canadian B/CB meeting. Step 2: Creation of a Canadian B/CB Society Step 3: Position the B/CB community for future funding opportunities
- 20. Strategic Objective 2: Strengthening and Sustaining the B/CB Research Enterprise
- 21. Strengthening and Sustaining the B/CB Research Enterprise Step 1: Organization of a workshop to bring together the B/CB researchers funded in the ongoing B/CB-focused initiatives Step 2: Development of a five-year coordinated plan among funding agencies and infrastructure providers Step 3: Development of activities/opportunities to support the integration of B/CB professionals and hardware providers into large-scale life sciences projects generating big data and requiring significant data storage and analysis.
- 22. Strategic Objective 3: Building Capacity
- 23. Building Capacity: Connect, Coordinate and Train Step 1: The launch of innovative new graduate and postdoctoral training programs Step 2: Creation of new training opportunities and salary awards embedded in ongoing large-scale projects Step 3: Development and promotion of new opportunities for undergraduates Step 4 Support bioinformatics.ca series.
- 27. Cancer Genome Collaboratory • Making a sustainable infrastructure for cancer genome research. • A place to compute and collaborate on human cancer genome data in a secure way.
- 34. ( ICGC … https://icgc.org/ http://icgc.org/icgc/media
- 35. ( ICGC … • ICGC to collect: • DNA, RNA, methylomes and clinical data from 50 different tumour types. • 500 tumour/normals per tumour type • 25,000 (50,000) genomes • 1:10 (whole genome: exam) • SNV, CNV, SV, germline
- 39. Deliverable for PCAWG will include: • 1st PANCANCER analysis on > 2,800 cancer tumours from a WGS perspective • RNA, SSM, CNV, Methylation analysis & germline • Published (executable) pipelines • Docker / Dockstore • Mutiple cloud access to data • Multiple portal access to data • Many paper (being written & submitted now!)
- 40. PCAWG
- 46. PCAWG pipelines on Dockstore
- 48. Lessons Learned (1/2) • Be patient • You need to publish your “stuff” (“to make publicly or generally known” https://goo.gl/SgSV6R). • Publish your tools, SOPs, workflows, pipelines. • Virtualization of services, tools and resources • Shared APIs • Good infrastructure is critical, but good data even more so.
- 49. Lessons Learned (2/2) • Important to establish great tools and databases, but even more important to maintain them long term. • Lack of funding in Canada for maintenance of a resource (database) and the maintenance of a tool (service). • Training is critical, and you cannot have enough of it. We all need to do it (every country, every language). • Long term support • Do all this, and then tweet about it!
- 50. Lessons Learned (2/2) • Important to establish great tools and databases, but even more important to maintain them long term. • Lack of funding in Canada for maintenance of a resource (database) and the maintenance of a tool (service). • Training is critical, and you cannot have enough of it. We all need to do it (every country, every language). • Long term support • Do all this, and then tweet about it!
- 51. Acknowledgements B/CB Advisory Committee Gary Bader, U of Toronto Robert Beiko, Dalhousie U. Guillaume Bourque, McGill U. Fiona Brinkman, SFU Michael Brudno, U of Toronto Liz Conibear, UBC Bill Crosby, U Windsor Mark Dietrich, Compute Canada Francis Ouellette, OICR Peter Wilenius, CANARIE Cancer Genome Collaboratory Lincoln Stein, U of Toronto Guillaume Bourque, McGill U. Paul Boutros, U of Toronto Khaled el Emam, U of Ottawa Vincent Ferretti, OICR Bartha Knoppers, McGill U. Francis Ouellette, U of Toronto Cenk Sahinalp, SFU Sohrab Shah, UBC https://goo.gl/3wsGui