What funding? Building an multi- and interdisciplinary research program in Canada
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The document discusses building an interdisciplinary bioinformatics research program in Canada. It describes the author's experience obtaining multidisciplinary training and pursuing interdisciplinary research. It outlines goals such as developing practical skills, becoming knowledgeable, improving communication skills, and publishing research. The author discusses bioinformatics as an emerging area with few qualified individuals and the need to empower researchers and overcome specialization barriers.
What funding? Building an multi- and interdisciplinary research program in Canada
- 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
- 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
- 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
- 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
- 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!
- 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