ouellette elixir 2017

Reflections on Life Science Data

Infrastructures in Canada

Rome, March 20, 2017 B.F. Francis OuelletteCSO / VP Scientific Affairs, Génome Québec Montréal, QC, Canadafrancis@genomequebec.com

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.

in Memory of Anna Tramontano

https://goo.gl/UMBW8f

Outline of my Reflections

• The Parameters: “Made in Canada”• Building a National Bioinformatics Strategy

for Canada• The Cancer Genome Collaboratory• Lessons Learned

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.

… 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

Why a strategy?

• Genome Canada• CIHR• NSERC• SSHRC

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

Why a strategy?

• Genome Canada• CIHR• NSERC• SSHRC

• CFI• Compute Canada• CANARIE• Universities• Private sector

http://www.elixir-europe.org/

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

small expert steering committee

SESC + community

workshop

SESC + stakeholder

workshop

Largercommunity

consult

SESC + community

workshop

stakeholder & community

consult

SESC + community

workshop

Finisheddocument

2015

SESC + community

workshop

SESC + writer >Strategic

Plan

Strategic Objective 1: Networking and Coordination

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

http://www.nce-rce.gc.ca/

Strategic Objective 2: Strengthening and Sustaining the B/CB Research Enterprise

Strengthening and Sustaining

the B/CB Research EnterpriseStep 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.

Strategic Objective 3: Building Capacity

Building Capacity: Connect, Coordinate and

TrainStep 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.

Bioinformatics.ca workshops Content

http://bioinformatics-ca.github.io/

https://goo.gl/CGu13q

https://goo.gl/CGu13q

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.

https://www.cancercollaboratory.org/

Cancer Genome Collaboratory

https://goo.gl/nLlVKf

Cancer Genome Collaboratory

https://www.cancercollaboratory.org/

Cancer Genome Collaboratory

https://www.cancercollaboratory.org/

Cancer Genome Collaboratory

https://www.cancercollaboratory.org/

Cancer Genome Collaboratory

https://www.cancercollaboratory.org/about-collaboratory

( ICGC …

https://icgc.org/ http://icgc.org/icgc/media

( 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

…ICGC)

https://dcc.icgc.org/

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!)

PCAWG

Cancer Genome Collaboratory

Vincent Ferretti https://goo.gl/cSW7bD

Vincent Ferretti https://goo.gl/cSW7bD

http://dockstore.org

PCAWG pipelines on Dockstore

Training available:https://goo.gl/tGmSYW

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.

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!

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!

Acknowledgements

B/CB Advisory CommitteeGary Bader, U of TorontoRobert Beiko, Dalhousie U.Guillaume Bourque, McGill U.Fiona Brinkman, SFUMichael Brudno, U of TorontoLiz Conibear, UBCBill Crosby, U WindsorMark Dietrich, Compute CanadaFrancis Ouellette, OICRPeter Wilenius, CANARIE

Cancer Genome CollaboratoryLincoln Stein, U of TorontoGuillaume Bourque, McGill U.Paul Boutros, U of TorontoKhaled el Emam, U of OttawaVincent Ferretti, OICRBartha Knoppers, McGill U.Francis Ouellette, U of TorontoCenk Sahinalp, SFUSohrab Shah, UBChttps://goo.gl/3wsGui