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Celebrating 25 years of bioinformatics.ca

BF Francis Ouellette

Montréal, July 13, 2024

Education track, ISMB2024

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2

Module #: Title of Module

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1999 to 2024: �169 CBW workshops delivered

CGDN - UBC

OICR

McGill

OICR-2

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Outline

Assessment of need for workshops
Delivering the 1^st workshop
Plan for the other 168 +
Most important assets
Lessons learned

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https://shrtm.nu/pu1vZ11

https://shrtm.nu/Vfk6bpZ

1993-1998

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1998-2007

Vancouver, BC

Michael Hayden

Phil Hieter

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Task force, 1st workshop: Mission creep! (1/2)

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Task force, 1st workshop: Mission creep! (2/2)

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Francois Major, U de Montréal

Chris Hogue, MSH

Christoph Sensen, NRC

Francis Ouellette, CMMT, UBC

Stephen Herst, CGDN

David Wishart, U of Alberta

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Halifax, NRC, 1998

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Model we started with, and still mostly in use:

Lecture Topic 1

Lab Topic 1

Lecture Topic 2

Lab Topic 2

Lunch on your own

Provide coffee

Provide breakfast

Provide coffee

Dinner on your own

We called this a “Module”

Provided each student with:

Windows PC
UNIX server in the room
Printed Lecture notes (2X4” binders)
CBW Mouse pad

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Modules at the 1^st 1999 workshop: 2 week-long

Week 1

Biology < > Computer Science
2 week-long multipart assignement presented
Databases (Entrez Lab)
Evolution
PERL (lab)
BLAST (theory, practice and installation)
Alignment/CLUSTAL W
GCG
RNA Translation

Week 2

DNA and Nucleic Acid patterns
Genome Analysis (Magpie)
Cell trafficking, and Model Organisms (SGD lab)
DNA to protein (Peptool Lab)
3D structures
Sequence to function
Motifs to Domains (Rasmol lab)
Structure prediction
RNA databases & Modeling
RNA motifs & RNA 3D models

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2 weeks

1 week

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Intro to Proteomics
Mass Spectrometry (+lab)
Protein Databases
Protein Structure
Protein-Protein interactions
Homology modeling
Threading (+lab)
Structure Alignment

Proteomics

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SRS and Entrez
ACeDB
Sequence-ready Physical Mapping
Whole Genome Sequencing
WGS lab: lambda phage assembly
ESTs and Microarrays
SNP
Prokaryotic genome annotation
Eukaryotic gene finding

Genomics

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Sequence Comparison / Homology
Software Development practices (Jim Ostell)
Data Structures
Generating 2D Structure
Data Mining
Neural Network (Joshua Bengio)
Probabilistic Algorithms
Genetic Algorithm vs. Monte Carlo Assignment
Protein 3D Structure, NCBI Toolkit

Tools

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CBW Certificate

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Workshops in 1999 to 2007:

My Vancouver years
30 workshops in 8 years, ~ 1,250 BoS
9 Bioinformatics + 8 Genomics
7 Proteomics + 6 Developing the Tools + Intro to Programing

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http://goo.gl/ZKzMV

2007

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http://goo.gl/ZKzMV

2007

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Toronto

2007 - 2017
OICR: Ontario Institute for Cancer Research

PI and Associate Director to Lincoln Stein

Tom Hudson new director to the Ontario Institute for Cancer Research
Lincoln Stein is Director of BioComputing
I recruited Michelle Brazas as CBW PM, & she is also doing outreach for OICR.
OICR is committed to CBW and bioinformatics training!

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CGDN - UBC

OICR

McGill

OICR-2

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bioinformatics.ca @ OICR (2007 – 2017)

Needed a big change for the workshops:
New format, shorter (2-3 days)
More advanced topics (intro now covered by many universities)
New web development team.

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bioinformatics.ca @ OICR (2007 – 2017)

Introduction to R
Analysis Using R
Bioinformatics for Cancer Genomics
Epigenomics Analysis
High Throughput Sequencing
Machine Learning
Metabolomics Analysis
Microbiome Analysis
Pathway and Network Analysis
RNA-seq Analysis

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CBW is also not in a vacuum

Need to be aware of our Society

ISCB Education
GOBLET
Elixir-Europe and all of the Elixir Nodes

Need to ”publish”

Education articles in PLOS Comp. Biol. Or any other good journal!
On our respective websites

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CGDN - UBC

OICR

McGill

OICR-2

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2018-2021

I left OICR
Moved to Quebec
Workshops now headquartered at McGill with the support of Guillaume Bourque.
New position at GQ, then at the Neuro
2020 season of CBW had to shift to Virtual (COVID-19), same for 2021
Had to stop working on the CBW
I resigned from CBW in 2021
2022 season of CBW cancelled
Picked-up again in 2023 at the OICR

Keynote tomorrow AM ->

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CGDN - UBC

OICR

McGill

OICR-2

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2023 to present: OICR-2

I’m less involved, so this is from an outsider’s perspective
Michelle Brazas takes the lead, with the great help from Nia Hughes (CBW PM).
Very active uptake of workshops with a mix �of virtual and face to face.
We learn from our African friends, and do networked simultaneous venues.
New workshops are introduced

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Community comes together to remake a new CBW.
CIHR has a call:

$6,050,000 is available to fund an application relevant to Bioinformatics, Computational Biology, and Health Data Sciences pool. The maximum amount per grant is $1,008,333 per year for up to 6 years, for a total of $6,050,000 per grant.

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bioinformatics.ca 2.0

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50% of the 169 workshops in Toronto, �14% in Vancouver�8% Montréal�12% virtual�rest in 9 different �Canadian cities �+ 4 (2%) in USA (NY)

The “ca” in bioinformatics.ca

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Open Science

No Commercial software
Open course material
Open Data used in class
(challenges with controlled data)
FAIR training material
Video of lectures

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Things we have not done well so far�(but are planning)

Gender balance
Bilingual delivery.
Visible minorities
Indigenous nations (in Canada, USA, Australia, Brazil, and many others)
Distribute across Canada
Post-post workshop surveys

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Founding Faculty

Francis Ouellette (Vancouver)

Francois Major (Montreal)

Christopher Hogue (Toronto)

Christoph Sensen (Calgary)

David Wishart (Edmonton)

Guest Faculty:

Keith Ashman (Toronto)

David Baillie (Vancouver)

Andreas Baxevanis (Bethesda)

Ron Beavis (Winnipeg)

Fiona Brinkman (Vancouver)

Larry Greller (Kingston)

Dan Figeys (Toronto)

Phil Hieter (Vancouver)

Tom Hudson (Monteal)

Walid Houry (Toronto)

Steven Jones (Vancouver)

Marco Marra (Vancouver)

Gabor Marth (Bethesda)

Roberto Sanchez (New York)

Steve Scherer (Toronto)

John Wilbur (Bethesda)

From a 2003 presentation: Gender balance

TAs in 1999
Paul	Gordon
Sanja	Rogic
Stefanie	Butland
Ryan	Brinkman
Paul	Van Domselaar
Katerina	Michalikova
Sebastien	Lemieux

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Lessons learned to make bioinformatics.ca work:

Need a team of zealous people.
Need to know and understand your student population.
Need leadership, with institutions that support them.
Need to make a good product and be relevant.
Need to evolve (update/add/remove) with the science, and the teaching methods.
Need to have instructor that are representative of �the community you are serving.
Need to be Open.
Need to market your “product”.
Need to network with other instructors.
Need to train the next generation of instructors and empower them.

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Most important asset:

Since the beginning, it was clear that the most important asset of the CBW were the Instructors!

When a workshop is given
How often a workshop is given
How long and how simple or complicated: we would talk, but their feedback was essential.

We built an MNM (Mentor Network Meeting) and an EAB(Education Advisory Board), to advise, and also to make it clear their feedback was essential.

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One of the five founders of CBW.
University of Alberta Distinguished Professor.
https://en.wikipedia.org/wiki/David_S._Wishart
Computational biology and open science, Proteomics, Metabolomics, and Machine Learning.
The only one present throughout the last 25 years.
Some of the current CBW instructors were trained by him.
Best long standing CBW instructor <period>

David Wishart

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