Outline

1. Bioinformatics education at the Université de Montréalwww.bioinfo.umontreal.caFormation en bio-informatique à l’ Université de Montréal

2. Outline • Bioinformatics • Definition • Activities at UdeM • Shortage of skilled personnel • Training programs at UdeM • Fellowships at UdeM

3. Bioinformatics - definition • Data acquisition • Data storage & retrieval • Data analysis • Development of tools • Design of algorithms & methods

4. Bioinformatics activities at UdeM • History - Founders Robert Cedergren (Biochemistry) & David Sankoff (Mathematics, Computer Science): seminal paper on 5.8S rRNA (1976) in Nature • 10 major research groups in departments Biochemistry, Biology, Computer Science, Pediatry, Physics • Collaborations within Quebec, Canada and world-wide

5. Bioinformatics activities at UdeM • Research areas • Comparative genome analysis • Phylogenetic inference • Structure modeling & prediction • Databases • Modeling of molecular evolution • Algorithms & computational methods

6. Bioinformatics activities at UdeM • Some research groups and expertise • S.Chteinberg: RNA 2-D structure prediction; RNA-RNA interactions • G.Burger: Comparative genome analysis & software development; integrated databases • N.El-Mabrouk: Algorithmics of genome rearrangements; structure prediction • S.Hamel: Algorithmics of trees and 2-D structures • BF.Lang: Integrated databases; structure/function of sequence motifs • F.Major: RNA 3-D structure modeling • S.Mischnick: Protein-protein interaction • N.Mousseau: Algorithmics of protein folding • H.Philippe: Modeling of molecular evolution and tree robustness

7. Shortage of skilled bioinformaticians “Biologists are confronted by a tidal wave of information. Unfortunately, few of them know how to swim.” - Economist Magazine, 26 June, 1999 Sector Academic, private and public (R&D) sectors Skills • Data production process control • Database design, implementation, curation • Data analysis pipelines using existing tools • Development of tools • Design of algorithms & methods Sought education BSc<MSc≤PhD

8. Bioinformatics training programs at UdeM • Conception • Departments of Biochemistry & Computer Science • Aims • Solid training in both Computer & Life Sciences • Critical thinking • Initiative, creativity • Team player

9. Bioinformatics training programs at UdeM • Notable features • Trans-disciplinary courses • Theoretical and hands-on training • Problem-driven learning • Scientific communication • Autonomous research

10. Bioinformatics training at UdeM • Academic degree programs • Bachelor program (3 y) • Master’s program (2 y) • PhD program (3-4 y) • Post-doctoral training

11. Bioinformatics training at UdeM • Number of students (Fall 2003) • Bachelor program: 49 • Master’s program: 23 • PhD program: 9 • Post-docs: 12

12. Bioinformatics B.Sc. program at UdeM Common Block Biology, biochemistry, chemistry, computer science, mathematics, bioinformatics, ethics Option Life Science Structural biology, ecology, neuroscience.. Option Computer Science Mathematics, simulation, engineering, db systems.. Other Disciplines Law, management, sociology.. Autonomous Research 3-month internship

13. Bioinformatics B.Sc. program at UdeM • Conditions of admission • College Mathematics, Physics, Chemistry, Biology, or equivalent • Basic French language • Places 30 per year

14. Bioinformatics M.Sc. program at UdeM Preparative Studies Individualized plan Common Block Algorithmics & applications in bioinformatics Duration Preparative courses 0-2 trimester Regular courses 2 trimester Research/internship ~1 year Specialization Bioinformatics, computer & life science; mathematics Research Workshops Scientific approaches, communication Autonomous Research Academic project & thesis Internships 2 x 6-month in public or private sector

15. Bioinformatics M.Sc. program at UdeM • Conditions of admission • B.Sc. in either • Computer Science • Life Sciences • Mathematics • or similar • Supervisor • Basic French language • Number of places ~30

16. Bioinformatics Ph.D. program at UdeM Preparative Studies Individualized plan Duration Preparative courses 0-1 trimester Regular courses Concomitant (6 credits) Research ~2-4 years Research Workshops, Conferences Autonomous Research Academic project & thesis

17. Bioinformatics Ph.D. program at UdeM • Conditions of admission • M.Sc. in • Bioinformatics, or • Equivalent bi-disciplinary training • Supervisor • Number of places ~30

18. Bioinformatics fellowships at UdeM • biT – program of excellence • Funded by CIHR • $1,8 Mio over 6 years • Full financing of • Master’s & PhD studies • Post-doctoral training • Including preparative studies • Eligibility & Selection criteria • Enrolled at UdeM • Excellence in academic and/or professional performance

19. Bioinformatics ‘mobility’ programs • Study exchange programs with most French universities • Academic internship exchange programs esp. with Université de Poitiers & d’Aurillac • Private sector internship agreements • Co-supervision of graduate students with researchers outside UdeM

20. Programmes d’ étude en bio-informatique à l’ Université de MontréalResponsable: Gertraud Burgerwww.bioinfo.umontreal.ca