What funding?
Building a multi- and
interdisciplinary
research program
in Canada
Michel Dumontier, PhD
Associate Professor of Bioinformatics
Department of Biology, Institute of Biochemistry, School of Computer Science, Ottawa
Institute of Systems Biology, Ottawa-Carleton Institute of Biomedical Engineering
Carleton University
Schachter Memorial Lecture, University of Toronto, June 17, 2009

Past, Present and Future
• multidisciplinary beginnings
• graduate specialization
• interdisciplinary research
• next steps

Research Assistant: University of Manitoba
An extraordinary and eye-opening opportunity
The Golgi Apparatus : 3D reconstruction from serial-section TEM

Research Associate: Max Planck Institute
Learning and having fun while doing research
Role of small GTPase Rac in signalling and morphology

Mentor: Chris Hogue
Innovator & Provider of Opportunities

Graduate Student Experience:
Quite the ride!

Wife: Heather Farmer
Unwavering supporter

Goals
• Pursue interesting research
• Develop practical skills
• Become knowledgeable
• Improve communication skills
• Publish research
• Track progress

Develop skills and stand out

Bioinformatics
Emerging area
- high profile (HGP)
- few qualified individuals
- specialization barrier
Empowering

Quick n Dirty
Estimating the number of human genes
Jan 24, 2001
35000
y = 3995.4Ln(x) - 55156
30000
32000
25000
Number of Genes
20000
15000
10000
5000
0
1.00E+05 1.00E+06 1.00E+07 1.00E+08 1.00E+09 1.00E+10
Genom e Size (bp)
Feb 15, 2001 - 30,000–40,000 March 9, 2009 : 32,484

Knowledge Discovery:
A family of species-specific predictive tools
1
0.8
0.6 0.6
0.4 0.4
0.2 0.2
0 0
-0.2 -0.2
-0.4 -0.4
-0.6 -0.6
TYR VAL TYR
THR TRP
PRO SER SER
LYS MET PHE
ILE LEU -0.8
GLY HIS MET
GLN GLU
ASP CYS
ARG ASN ILE
S1
ALA -1
2D
ALA
ARG
ASN
GLU
ASP
CYS
GLN
GLU
GLY
HIS
ILE
LEU
ASP
LYS
MET
PHE
PRO
SER
THR
TRP
TYR
ALA
PEP
VAL
1D
3D

Chart your progress

John R. Glover
Régis Pomès
Julie Forman-Kay
The Committee:
At your service Walid A. Houry

Master the Art of Presentations
Engage your audience

Find exuberance in writing

Be a part of something bigger than you

You’re ready when you’re
pretty much independent
(and your committee agrees)

Post-Doc: Blueprint Initiative
Protein Small
Molecule Interactions
Hardware Accelerated
Protein Identification for Chemical Ontology
Tandem Mass Spectrometry

The Post-Doc
• chart a new direction
• result-oriented projects
• learn to write grants
• collaborate
• network

Career choices
• business
• government
• academia

Newly Minted Prof 

The
10 / 90
rule

Planning the Research Enterprise

Cellular Visions: The Inner Life of a Cell

Personalized Medicine
Knowledge Representation and Reasoning
Dynamic Systems Modeling and Simulation
Computational Drug Discovery
High Performance Computing

I want to make available our collective biochemical
knowledge for learning and answering questions
Web search engines just aren’t enough

Surface web:
167 terabytes
Deep web:
91,000 terabytes
545-to-one

Data silos – not made for sharing

The Semantic Web will expose data
and link knowledge

Competitive intelligence

Strategy

Interdisciplinary Research:
Biochemical Knowledge Representation and
Reasoning
Biochemistry
Computer
Logic
Science
Ontology

You want to join the knowledge web

Bio2RDF provides the
methodology to create and
glue these different
networks.

something you can lookup or
search for with rich descriptions

Ontology
as Strategy

OWL Has Explicit Semantics
Can therefore be used to captured knowledge in
a machine understandable way

Grant
writing

Few (can) see it your way

Paraphrasing
“unrealistic and overly ambitious research”
“proposes to solve problems that have been
worked on for decades”
“nothing particularly novel from a CS POV”
“requires a ontologist”

Grant Reviews on Interdisciplinary
Research

Pet: Killer
Psychological therapist

Carve out a more
focused proposal

You’ll (eventually) get funded
• it may be less than you asked for
• but you’ll be able to build a team
• and do the research you want to

$38,000
$19,200
$15,000

Building your team

Trust and Responsibility

Watching students learn and
develop is awesome

Balancing
innovative research
with
great teaching
is an
underappreciated
challenge

Teaching 101
Do you have what it takes to be a great teacher?

General Biochemistry I - Mid Term
25
20
% Students
15
10
5
0
Mean 52%±16

“It isn’t that you had bad questions,
you just had too many good ones”
Anthony Marini
Instructor
Faculty Teaching Certificate Program

BIOC3101 - Mark Distribution
14
12
10
8 midterm
makeup
6 current
4
2
0
0 10 20 30 40 50 60 70 80 90

Orchestrate
Tie teaching to research
Research is exciting to undergraduates!

Tenure and Promotion

Publish early
Publish often
Publish open

Next Steps
Knowledge Dissemination
Community Building
Knowledge Web

Agreement on data standards may be
contentious among stakeholders.

Share your data

Bridge your data
with others in
semantic
communities
(data networks).

Build a
knowledge base
from a series of questions

Plan for the future, but take it one step at a time
Develop your skills and expertise
Target an emerging area
Check your ambition
Think big.

My thanks to
• Family • Dumontier Lab
• Hogue Lab – Leonid Chepelev
– Natalia Villanueva-Rosales
• Advisory Committee – Alex De Leon
• Biochem Faculty – Mykola Konyk
– Jose Cruz
• BGSU – Glen Newton
• Drinking buddies – Alison Callahan
• Collaborators
• Carleton Faculty – Jim Green
– Jim Cheetham – Bill Willmore
– Bijan Parsia
– Carole Yauk & Paul White
– W3C HCLSIG /OWLWG
Slides - Scott Brinker @ Chief Marketing Technologies

dumontierlab.com
michel_dumontier@carleton.ca