Graduate Calendar 2008-2009

Ottawa-Carleton Collaborative Program in Bioinformatics

30 Marie Curie
Ottawa, ON K1N 6N5
Tel.: 613-562-5800

The Program

Coordinator: Stephane Aris-Brosou, Department of Biology, University of Ottawa
Associate Coordinator: Michel Dumontier, Department of Biology and School of Computer Science, Carleton University

Bioinformatics is an emerging and increasingly important scientific discipline dedicated to the pursuit of fundamental questions about the structure, function and evolution of biological entities through the design and application of computational approaches. Fundamental research in these areas is expected to increase our understanding of human health and disease which will translate to innovation in industry (i.e. drug discovery). As a field of research, it crosses traditional disciplinary boundaries such as computer science, chemistry, biology, biochemistry, engineering and the medical sciences. While individual researchers usually specialize in a particular area, bioinformaticians today must be able to appreciate significant research in other fields and therefore require an understanding of the basic principles of other disciplines. To meet this challenge Carleton University and the University of Ottawa offer a collaborative program leading to a Master of Science degree with Specialization in Bioinformatics or Master of Computer Science degree with Specialization in Bioinformatics.

Participating Institutes and Departments

The primary degree-granting units are:

• The Ottawa-Carleton Institute of Biology, the joint graduate program of the departments of Biology at the University of Ottawa and Carleton University
• The Ottawa-Carleton Institute of Computer Science, the joint graduate program of the School of Information Technology at the University of Ottawa and of the department of Computer Science at Carleton University
• The Ottawa-Carleton Institute of Mathematics and Statistics, the joint graduate program of the department of Mathematics and Statistics at the University of Ottawa and of the School of Mathematics and Statistics at Carleton University
• The Cellular and Molecular Medicine graduate program of the Department of Cellular and Molecular Medicine (CMM) at the University of Ottawa

The Biochemistry graduate program and the Microbiology & Immunology graduate program of the Department of Biochemistry, Immunology and Microbiology at the University of Ottawa.

The collaborative program is managed by a committee made up of representatives of the various participating units. A director and associate director administer the program.

Members of the Collaborative Program

• S. Aris-Brosou, Computational molecular evolution, Ottawa-Carleton Institute of Biology, University of Ottawa
• K. Baetz, Yeast functional and chemical genomics, chromosome stability, identification of drug mode of action, Biochemistry, Microbiology and Immunology, University of Ottawa
• L. Bertossi, Database systems, data integration, computational logic, Ottawa-Carleton Institute of Computer Science, Carleton University
• J. Cheetham, Membrane biochemistry, Ottawa-Carleton Institute of Biology, Carleton University
• F. Dehne, Parallel computing, Ottawa-Carleton Institute of Computer Science, Carleton University
• G. Drouin, Evolution of multi gene families, concerted evolution, gene conversion, Ottawa-Carleton Institute of Biology, University of Ottawa
• M. Dumontier, Semantic web, drug discovery, cell simulation, hardware acceleration, Ottawa-Carleton Institute of Biology, Ottawa-Carleton Institute of Computer Science, Carleton University
• D. Figeys, Proteomics, mass spectrometry, Biochemistry, Microbiology and Immunology University of Ottawa
• A. Golshani, Proteomics, functional genomics, Ottawa-Carleton Institute of Biology, Carleton University
• R. Gorelick, Evolutionary theory, Ottawa-Carleton Institute of Biology, Ottawa-Carleton Institute of Mathematics and Statistics, Carleton University
• J. Green, Protein structure prediction, data mining, Systems and Computer Engineering, Ottawa-Carleton Institute of Computer Science, Carleton University
• M. Kaern, Gene networks, Cellular & Molecular Medicine, University of Ottawa
• E. Kranakis, Analysis of algorithms, computational and combinatorial geometry, distributed computing, and network security, Ottawa-Carleton Institute of Computer Science, Carleton University
• V. Pestov, Topological transformation groups, geometry of large dimensions, Ottawa-Carleton Institute of Mathematics and Statistics, Carleton University
• D. Sankoff, Mathematical genomics, Ottawa-Carleton Institute of Mathematics and Statistics, University of Ottawa
• S. Sinha, Robust inference, time series analysis, biostatistics, longitudinal data analysis, Ottawa-Carleton Institute of Mathematics and Statistics, Carleton University
• A. Stintzi, Microbial genomics, gene expression and regulation, microarray and functional genomics, Biochemistry, Microbiology and Immunology University of Ottawa
• M. Turcotte, Bioinformatics, algorithm design, applications of machine learning, Ottawa-Carleton Institute of Computer Science, University of Ottawa
• G. Wainer, DEVS formalism, real-time modelling, cellular models, parallel / distributed / web-based simulation, Systems and Computer Engineering, Ottawa-Carleton Institute of Computer Science, Carleton University
• X. Xia, Genomics, evolutionary molecular genetics, molecular phylogenetics, Ottawa-Carleton Institute of Biology, Carleton University

Master’s Program

Application to the Program

Applications should be directed to the primary participating unit which is the most appropriate to the student's research interests. Once accepted into one of the participating graduate programs, students must then be sponsored into the collaborative program in Bioinformatics by a faculty member. This is normally the student’s supervisor. This faculty member must be appointed, cross-appointed or stand as an adjunct at one or more of the participating units.

The program operates within the general framework of the "Regulations and Procedures for Joint Graduate Programs" (www.ocjip.ca) and the general regulations of the graduate faculty at each of the two universities.

Application forms and further information can be obtained by writing directly to any of the participating institutes or departments, or the program coordinator.

Admission Requirements

The requirements for admission to the master's in the Collaborative Program in Bioinformatics are as follows:

• prior admission to the master's program in one of the supporting units participating in the program.
• a letter of recommendation from the participating faculty member of the Collaborative Program, which both recommends admission and indicates the willingness of the faculty member to supervise the candidate's research program in Bioinformatics.

Program Requirements

The student is responsible for fulfilling both the participating unit requirements for the Master’s degree, and the requirements of the Collaborative Program.

The minimum requirements of the collaborative program include successful completion of two required courses, and a master’s thesis on an approved bioinformatics topic.

A three-credit course at the University of Ottawa is equivalent to a 0.5 credit course at Carleton University.

• BIOL 5515 Bioinformatics  (0.5 credit)
• BIOL 5517 Bioinformatics Seminar (0.5 credit)

Students in programs in Biology, Computer Science, Mathematics & Statistics may use BIOL 5515 Bioinformatics to count towards degree requirements; BIOL 5517 Bioinformatics Seminar must be taken in addition to the regular seminar course.

In addition, the student’s thesis committee or advisory committee may direct the student to take or audit further courses to complement the student’s background and research program.

Thesis

Candidates must successful complete a research thesis on a topic in bioinformatics supervised by a faculty member of the Collaborative Program in Bioinformatics.

Graduate Courses

Required Courses

BIOL 5515 [0.5 credit] (BNF 5106)
Bioinformatics
Major concepts and methods of Bioinformatics.  Topics may include, but are not limited to:  genetics, statistics and probability theory, alignments, phylogenetics, genomics, data mining, protein structure, cell simulation and computing.

BIOL 5517 [0.5 credit] (BNF 6100)
Bioinformatics Seminar
Current topics in bioinformatics.  Students must successfully complete a presentation and written report. 

Other Courses