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What funding?
Building a multi- and
interdisciplinary
research program
in Canada




Michel Dumontier, PhD
Associate Profe...
Past, Present and Future
• multidisciplinary beginnings
• graduate specialization
• interdisciplinary research
• next steps
Research Assistant: University of Manitoba
                             An extraordinary and eye-opening opportunity




 ...
Research Associate: Max Planck Institute
                       Learning and having fun while doing research




         ...
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
• Pub...
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
                                        ...
Knowledge Discovery:
            A family of species-specific predictive tools



                                        ...
Chart your progress
John R. Glover




   Régis Pomès



                  Julie Forman-Kay


The Committee:
At your service                  ...
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 Int...
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...
I want to make available our collective biochemical
knowledge for learning and answering questions




 Web search engines...
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

                 Biochemist...
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 decade...
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 ...
$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


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

                          Anthony Marini
        ...
BIOC3101 - Mark Distribution

14


12


10


 8                                                          midterm
         ...
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

               ...
My thanks to
•   Family                  • Dumontier Lab
•   Hogue Lab                     –   Leonid Chepelev
           ...
dumontierlab.com
michel_dumontier@carleton.ca
What funding? Building an multi- and interdisciplinary research program in Canada
What funding? Building an multi- and interdisciplinary research program in Canada
What funding? Building an multi- and interdisciplinary research program in Canada
What funding? Building an multi- and interdisciplinary research program in Canada
What funding? Building an multi- and interdisciplinary research program in Canada
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What funding? Building an multi- and interdisciplinary research program in Canada

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What funding? Building an multi- and interdisciplinary research program in Canada

  1. 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. 2. Past, Present and Future • multidisciplinary beginnings • graduate specialization • interdisciplinary research • next steps
  3. 3. Research Assistant: University of Manitoba An extraordinary and eye-opening opportunity The Golgi Apparatus : 3D reconstruction from serial-section TEM
  4. 4. Research Associate: Max Planck Institute Learning and having fun while doing research Role of small GTPase Rac in signalling and morphology
  5. 5. Mentor: Chris Hogue Innovator & Provider of Opportunities
  6. 6. Graduate Student Experience: Quite the ride!
  7. 7. Wife: Heather Farmer Unwavering supporter
  8. 8. Goals • Pursue interesting research • Develop practical skills • Become knowledgeable • Improve communication skills • Publish research • Track progress
  9. 9. Develop skills and stand out
  10. 10. Bioinformatics Emerging area - high profile (HGP) - few qualified individuals - specialization barrier Empowering
  11. 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. 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. 13. Chart your progress
  14. 14. John R. Glover Régis Pomès Julie Forman-Kay The Committee: At your service Walid A. Houry
  15. 15. Master the Art of Presentations Engage your audience
  16. 16. Find exuberance in writing
  17. 17. Be a part of something bigger than you
  18. 18. You’re ready when you’re pretty much independent (and your committee agrees)
  19. 19. Post-Doc: Blueprint Initiative Protein Small Molecule Interactions Hardware Accelerated Protein Identification for Chemical Ontology Tandem Mass Spectrometry
  20. 20. The Post-Doc • chart a new direction • result-oriented projects • learn to write grants • collaborate • network
  21. 21. Career choices • business • government • academia
  22. 22. Newly Minted Prof 
  23. 23. The 10 / 90 rule
  24. 24. Planning the Research Enterprise
  25. 25. Cellular Visions: The Inner Life of a Cell
  26. 26. Personalized Medicine Knowledge Representation and Reasoning Dynamic Systems Modeling and Simulation Computational Drug Discovery High Performance Computing
  27. 27. I want to make available our collective biochemical knowledge for learning and answering questions Web search engines just aren’t enough
  28. 28. Surface web: 167 terabytes Deep web: 91,000 terabytes 545-to-one
  29. 29. Data silos – not made for sharing
  30. 30. The Semantic Web will expose data and link knowledge
  31. 31. Competitive intelligence
  32. 32. Strategy
  33. 33. Interdisciplinary Research: Biochemical Knowledge Representation and Reasoning Biochemistry Computer Logic Science Ontology
  34. 34. You want to join the knowledge web
  35. 35. Bio2RDF provides the methodology to create and glue these different networks.
  36. 36. something you can lookup or search for with rich descriptions
  37. 37. Ontology as Strategy
  38. 38. OWL Has Explicit Semantics Can therefore be used to captured knowledge in a machine understandable way
  39. 39. Grant writing
  40. 40. Few (can) see it your way
  41. 41. 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”
  42. 42. Grant Reviews on Interdisciplinary Research
  43. 43. Pet: Killer Psychological therapist
  44. 44. Carve out a more focused proposal
  45. 45. 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
  46. 46. $38,000 $19,200 $15,000
  47. 47. Building your team
  48. 48. Trust and Responsibility
  49. 49. Watching students learn and develop is awesome
  50. 50. Balancing innovative research with great teaching is an underappreciated challenge
  51. 51. Teaching 101 Do you have what it takes to be a great teacher?
  52. 52. General Biochemistry I - Mid Term 25 20 % Students 15 10 5 0 Mean 52%±16
  53. 53. “It isn’t that you had bad questions, you just had too many good ones” Anthony Marini Instructor Faculty Teaching Certificate Program
  54. 54. BIOC3101 - Mark Distribution 14 12 10 8 midterm makeup 6 current 4 2 0 0 10 20 30 40 50 60 70 80 90
  55. 55. Orchestrate Tie teaching to research Research is exciting to undergraduates!
  56. 56. Tenure and Promotion
  57. 57. Publish early Publish often Publish open
  58. 58. Next Steps Knowledge Dissemination Community Building Knowledge Web
  59. 59. Agreement on data standards may be contentious among stakeholders.
  60. 60. Share your data
  61. 61. Bridge your data with others in semantic communities (data networks).
  62. 62. Build a knowledge base from a series of questions
  63. 63. 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.
  64. 64. 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
  65. 65. dumontierlab.com michel_dumontier@carleton.ca

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