what funding? building an multi- and interdisciplinary research program in canada
TRANSCRIPT
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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
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Past, Present and Future
• multidisciplinary beginnings • graduate specialization• interdisciplinary research• next steps
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Research Assistant: University of ManitobaAn extraordinary and eye-opening opportunity
The Golgi Apparatus : 3D reconstruction from serial-section TEM
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Research Associate: Max Planck Institute
Role of small GTPase Rac in signalling and morphology
Learning and having fun while doing research
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Mentor: Chris HogueInnovator & Provider of Opportunities
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Graduate Student Experience:
Quite the ride!
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Wife: Heather FarmerUnwavering supporter
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Goals
• Pursue interesting research• Develop practical skills• Become knowledgeable• Improve communication skills• Publish research • Track progress
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Develop skills and stand out
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Emerging area - high profile (HGP) - few qualified individuals - specialization barrier
Empowering
Bioinformatics
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y = 3995.4Ln(x) - 55156
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Genom e Size (bp)
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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
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Chart your progress
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Régis Pomès
Julie Forman-Kay
Walid A. Houry
John R. Glover
The Committee: At your service
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Master the Art of PresentationsEngage your audience
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Find exuberance in writing
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Be a part of something bigger than you
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You’re ready when you’re pretty much independent
(and your committee agrees)
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Post-Doc: Blueprint Initiative
Hardware Accelerated Protein Identification for Tandem Mass Spectrometry
Chemical Ontology
Protein Small Molecule Interactions
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The Post-Doc
• chart a new direction• result-oriented projects• learn to write grants• collaborate• network
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Career choices
• business• government• academia
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Newly Minted Prof
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The10 / 90
rule
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Planning the Research Enterprise
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Cellular Visions: The Inner Life of a Cell
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Knowledge Representation and Reasoning
Dynamic Systems Modeling and Simulation
Computational Drug Discovery
High Performance Computing
Personalized Medicine
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I want to make available our collective biochemical knowledge for learning and answering questions
Web search engines just aren’t enough
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Surface web:167 terabytes
Deep web:91,000 terabytes
545-to-one
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Data silos – not made for sharing
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The Semantic Web will expose data and link knowledge
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Competitive intelligence
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Strategy
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Biochemistry
Computer Science
Ontology
Logic
Interdisciplinary Research: Biochemical Knowledge Representation and
Reasoning
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You want to join the knowledge web
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Bio2RDF provides the methodology to create and glue these different networks.
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something you can lookup or search for with rich descriptions
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Ontology as Strategy
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OWL Has Explicit Semantics
Can therefore be used to captured knowledge in a machine understandable way
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Grant writing
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Few (can) see it your way
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“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
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Grant Reviews on Interdisciplinary Research
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Pet: KillerPsychological therapist
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Carve out a more focused proposal
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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
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$15,000
$19,200
$38,000
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Building your team
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Trust and Responsibility
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Watching students learn and develop is awesome
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Balancing innovative research
with great teaching
is an underappreciated
challenge
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Teaching 101
Do you have what it takes to be a great teacher?
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Mean 52%±16
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General Biochemistry I - Mid Term%
Stu
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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
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BIOC3101 - Mark Distribution
0
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midterm
makeup
current
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Orchestrate
Research is exciting to undergraduates!
Tie teaching to research
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Tenure and Promotion
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Publish early Publish oftenPublish open
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Next Steps
Knowledge DisseminationCommunity Building
Knowledge Web
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Agreement on data standards may be contentious among stakeholders.
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Share your data
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Bridge your data with others in semantic communities (data networks).
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Build aknowledge basefrom a series of questions
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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.
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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