What funding? Building an multi- and interdisciplinary research program in Canada
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Transcript of What funding? Building an multi- and interdisciplinary research program in Canada
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
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Genom e Size (bp)
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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
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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
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General Biochemistry I - Mid Term%
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“It isn’t that you had bad questions, you just had too many good ones”
Anthony MariniInstructor
Faculty Teaching Certificate Program
BIOC3101 - Mark Distribution
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makeup
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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