What funding?Building a multi- and interdisciplinary research programin Canada

Michel Dumontier, PhDAssociate Professor of BioinformaticsDepartment of Biology, Institute of Biochemistry, School of Computer Science, Ottawa Institute of Systems Biology, Ottawa-Carleton Institute of Biomedical EngineeringCarleton 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 ManitobaAn extraordinary and eye-opening opportunity

The Golgi Apparatus : 3D reconstruction from serial-section TEM

Research Associate: Max Planck Institute

Role of small GTPase Rac in signalling and morphology

Learning and having fun while doing research

Mentor: Chris HogueInnovator & Provider of Opportunities

Graduate Student Experience:

Quite the ride!

Wife: Heather FarmerUnwavering supporter

Goals

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

Develop skills and stand out

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

Empowering

Bioinformatics

y = 3995.4Ln(x) - 55156

0

5000

10000

15000

20000

25000

30000

35000

1.00E+05 1.00E+06 1.00E+07 1.00E+08 1.00E+09 1.00E+10

Genom e Size (bp)

Nu

mb

er o

f G

enes

March 9, 2009 : 32,484

Jan 24, 2001

Feb 15, 2001 - 30,000–40,000

32000

Quick n DirtyEstimating the number of human genes

A

LA

A

RG

A

SN

A

SP

C

YS

G

LN

G

LU

G

LY

H

IS

IL

E

LE

U

LY

S

M

ET

P

HE

P

RO

S

ER

T

HR

T

RP

T

YR

V

AL

P

EP ALA

ASP

GLU

ILE

MET

SER

TYR

-1

-0.8

-0.6

-0.4

-0.2

0

0.2

0.4

0.6

0.8

1

ALA ARG ASN ASP CYS GLN GLU GLY HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL

S1

-0.6

-0.4

-0.2

0

0.2

0.4

0.6

1D

2D

3D

Knowledge Discovery:A family of species-specific predictive tools

Chart your progress

Régis Pomès

Julie Forman-Kay

Walid A. Houry

John R. Glover

The Committee: At your service

Master the Art of PresentationsEngage 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

Hardware Accelerated Protein Identification for Tandem Mass Spectrometry

Chemical Ontology

Protein Small Molecule Interactions

The Post-Doc

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

Career choices

• business• government• academia

Newly Minted Prof

The10 / 90

rule

Planning the Research Enterprise

Cellular Visions: The Inner Life of a Cell

Knowledge Representation and Reasoning

Dynamic Systems Modeling and Simulation

Computational Drug Discovery

High Performance Computing

Personalized Medicine

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

Biochemistry

Computer Science

Ontology

Logic

Interdisciplinary Research: Biochemical Knowledge Representation and

Reasoning

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

“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”

Paraphrasing

Grant Reviews on Interdisciplinary Research

Pet: KillerPsychological 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

$15,000

$19,200

$38,000

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?

Mean 52%±16

0 0 10 20 30 40 50 60 70 80 90 100

0

5

10

15

20

25

General Biochemistry I - Mid Term%

Stu

de

nts

“It isn’t that you had bad questions, you just had too many good ones”

Anthony MariniInstructor

Faculty Teaching Certificate Program

BIOC3101 - Mark Distribution

0

2

4

6

8

10

12

14

0 10 20 30 40 50 60 70 80 90

midterm

makeup

current

Orchestrate

Research is exciting to undergraduates!

Tie teaching to research

Tenure and Promotion

Publish early Publish oftenPublish open

Next Steps

Knowledge DisseminationCommunity 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 aknowledge basefrom 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 • Hogue Lab• Advisory Committee• Biochem Faculty• BGSU• Drinking buddies

• Carleton Faculty– Jim Cheetham

• Dumontier Lab– Leonid Chepelev– Natalia Villanueva-Rosales– Alex De Leon– Mykola Konyk– Jose Cruz– Glen Newton– Alison Callahan

• Collaborators– Jim Green– Bill Willmore– Bijan Parsia– Carole Yauk & Paul White– W3C HCLSIG /OWLWG

Slides - Scott Brinker @ Chief Marketing Technologies

dumontierlab.commichel_dumontier@carleton.ca