1. 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

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

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

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

5. Mentor: Chris Hogue
Innovator & Provider of Opportunities

6. Graduate Student Experience:
Quite the ride!

7. Wife: Heather Farmer
Unwavering supporter

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

9. Develop skills and stand out

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

11. 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

12. 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

13. Chart your progress

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

15. Master the Art of Presentations
Engage your audience

16. Find exuberance in writing

17. Be a part of something bigger than you

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

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

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

22. Career choices
• business
• government
• academia

23. Newly Minted Prof 

25. The
10 / 90
rule

26. Planning the Research Enterprise

27. Cellular Visions: The Inner Life of a Cell

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

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

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

31. Data silos – not made for sharing

32. The Semantic Web will expose data
and link knowledge

33. Competitive intelligence

34. Strategy

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

36. You want to join the knowledge web

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

38. something you can lookup or
search for with rich descriptions

39. Ontology
as Strategy

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

41. Grant
writing

42. Few (can) see it your way

43. 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”

44. Grant Reviews on Interdisciplinary
Research

45. Pet: Killer
Psychological therapist

46. Carve out a more
focused proposal

47. 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

48. $38,000
$19,200
$15,000

49. Building your team

51. Trust and Responsibility

52. Watching students learn and
develop is awesome

53. Balancing
innovative research
with
great teaching
is an
underappreciated
challenge

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

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

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

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

59. Orchestrate
Tie teaching to research
Research is exciting to undergraduates!

60. Tenure and Promotion

61. Publish early
Publish often
Publish open

62. Next Steps
Knowledge Dissemination
Community Building
Knowledge Web

63. Agreement on data standards may be
contentious among stakeholders.

64. Share your data

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

67. Build a
knowledge base
from a series of questions

68. 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.

69. 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

70. dumontierlab.com
michel_dumontier@carleton.ca