Ottawa-Carleton Collaborative Program
in Bioinformatics
Ottawa-Carleton Collaborative Program in Bioinformatics
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1) Listing
i)
Title and level
The Collaborative Program in Bioinformatics / Programme Collaboratif en
Bioinformatique offers the designation of “Specialization in Bioinformatics” to the
Master of Science degree and the Master of Computer Science degree leading to:
a) Master of Science degree with Specialization in Bioinformatics
or
b) Master of Computer Science degree with Specialization in Bioinformatics
ii)
Participating programs and OCGS appraisal status
The Collaborative Program is intended to augment the research and training that the
student receives through one of the Institutes, Departments or Schools participating in
the program. The participating 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
program is of “Good Quality” (10/24/2003).
The Ottawa-Carleton Institute of Computer Science, the joint graduate program of the
departments of Computer Science at Carleton University and the School of Information
Technology at University of Ottawa. The program is of “Good Quality” (06/22/2001).
Computer Science will undergo its next periodic appraisal in 2007-2008.
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
Carleton University. The program is of “Good Quality” (02/02/2006).
The Biochemistry graduate program of the Department of Biochemistry, Immunology
and Microbiology at the University of Ottawa. The program is of “Good Quality”
(10/24/2004).
The Microbiology & Immunology graduate program of the Department of
Biochemistry, Immunology and Microbiology at the University of Ottawa. The
program is of “Good Quality with Report” (04/2005), with a report due in 2008.
The Cellular and Molecular Medicine graduate program of the Department of Cellular
and Molecular Medicine at the University of Ottawa. The program is of “Good
Quality” (10/05/2004).
Other interested units with master’s thesis graduate programs may be added in the
future.
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2) Focus and description of the collaborative program
i)
Bioinformatics as an intellectual focus
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. Bioinformatics is interdisciplinary in that it requires the integration of
knowledge about biology, biochemistry, mathematics and statistics and computer
science. Bioinformatics enhances purely experimental sciences by providing unique
insights by the analysis and prediction of biological behavior. Fundamental research in
these areas is expected to create new discoveries towards increasing our understanding
of human health and disease which will translate to innovation in industry (i.e. drug
discovery). To support this discovery and innovation pipeline, Carleton University and
the University of Ottawa propose to offer a Collaborative Program in the participating
units leading to a Master’s degree with the added designation of “Specialization in
Bioinformatics”. Such a designation will serve to acknowledge the student’s
contribution to the discipline and open new avenues of post-graduate work
opportunities in both industry and academia.
ii)
Uniqueness of the Collaborative Program
This Collaborative Program is unique in that it i) is a joint collaboration between 2
universities, 3 faculties and 9 units, ii) promotes interdisciplinary research and teaching
collaboration and iii) encourages research and graduate level training in the area of
Bioinformatics. The synergy resulting from the collaboration of these diverse
disciplinary-based departments is expected to produce a stimulating learning
environment, where Bioinformatics students will benefit from having faculty members
from the different participating units contribute to their learning experience through
research activities and courses. As well, some of the courses will be taught in both
official languages, thereby making it the first bilingual program in Bioinformatics in
Canada.
Interdisciplinary learning opportunities will occur by offering a new Bioinformatics
course and seminar taught by several faculty members from across the participating
units. The course coordinator will ensure that each lecture is well integrated with the
overall course objectives. To help support course integration, each lecture will consist
of a short general introduction and will relate to previously covered material. A new
seminar course will promote student learning with presentations and discussions of
current topics in Bioinformatics. These topics will be based both on research papers and
on the students’ own research. Researchers from other institutions will also be invited
to present their research.
iii)
Demand for Collaborative Program
The demand for this program will initially stem from current students of members of
the collaborative program. The nineteen members of the collaborative program have a
total of thirty graduate students who are interested in pursuing this specialization.
Program enrolments are expected to double grow from 30 to 60 within five years due to
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i) net increases in graduate student enrolment of existing members, particularly from
new faculty members who have yet to complete their student recruitment, ii) students of
non-core members who plan to work on Bioinformatics-related projects (approximately
10-15). It is expected that advertising of program in the graduate calendar for each
participating unit will highlight this research activity and capture the interest of new
and existing students.
iv)
Comparison with other regional efforts
The University of Toronto offers a PhD only collaborative program in Proteomics and
Bioinformatics among seven participating units. Hence, the proposed collaborative
program offers an alternative for students to obtain a specialization in Bioinformatics at
the Master’s level. A collaborative program in Bioinformatics at the University of
Montreal does exist at both the Master’s and Doctoral level, but is a French language
only program. McGill University offers a graduate option in Bioinformatics, whose
spirit and nature is similar to that which is proposed here, but is restricted to a single
institution.
This program is also distinct, yet complementary, to the efforts by the Ottawa Institute
for Systems Biology towards a stand-alone graduate program in Systems Biology.
Systems Biology aims to build predictive models of biological systems based on
experimental results that determine the relationships and interactions between various
parts of a biological system. Training in Bioinformatics will facilitate data integration,
analysis and prediction towards biological modeling of systems biology data.
3) Requirements of the collaborative program
i)
Application to the Collaborative Program
Applications should be directed to the primary participating unit that is the most
appropriate to the student’s background research interests and background degree(s).
Once sponsored and accepted into one of the graduate programs, students must then be
sponsored into the Collaborative Program in Bioinformatics by a faculty member in any
of the participating units. This is normally the supervisor.
ii)
Admission Requirements
The requirements for admission to the Collaborative Program are as follows:
1) Prior admission to the master’s program in one of the supporting units participating
in the program.
2) 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.
iii)
Degree 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
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requirements of the Collaborative Program include two course requirements and a
thesis requirement.
A) Course requirements
Students must take the following two courses:
1) Bioinformatics Course (BNF 5106 / BIO 5106 / BIOL 5XXX)
2) Bioinformatics Seminar (BNF 5XXX / BIO 5XXX / BIOL 5XXX)
Course requirements with respect to requirements of participating units
The Collaborative Program offered by Biology, Computer Science, Mathematics &
Statistics will allow the Bioinformatics Course to count towards unit requirements.
Therefore, the Bioinformatics Seminar is in addition to the unit requirements.
The Collaborative Program offered by Cellular & Molecular Medicine will allow
the Bioinformatics course to count towards degree requirements. The
Bioinformatics seminar may be taken in lieu of the CMM seminar. Therefore, no
additional courses are required in addition to unit requirements.
The Collaborative Program offered by Microbiology & Immunology requires that
students take the Bioinformatics course and the Bioinformatics Seminar in addition
to unit requirements. Therefore, two additional courses are in addition to unit
requirements.
B) Thesis requirements
Constituted according to the rules of the primary unit where the student is enrolled,
the thesis committees will include at least one member of the Collaborative
Program. This will help ensure that the direction and content of the thesis are
suitable to obtain the specialization.
Four months prior to the thesis defense, program participants will provide the
Coordinating Committee with a brief description (2 pages) of their thesis and how it
contributes to the field of Bioinformatics. Together with an official transcript
indicating the satisfactory fulfillment of course requirements, the Coordinating
Committee will vote on granting the designation of “Specialization in
Bioinformatics”.
4) Members of the Collaborative Program
All faculty members of the participating units with supervisory privileges may supervise
graduate students accepted in the collaborative program. Members of the Collaborative
Program are expected to participate in the teaching of the program courses and pursue
research in the field of Bioinformatics.
i)
Current Coordinator
Stéphane Aris-Brosou
Department of Biology
University of Ottawa
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ii)
Current Associate Coordinator
Michel Dumontier
Department of Biology and School of Computer Science
Carleton University
iii)
Current Members of the Collaborative Program
The research fields of the members of the Collaborative Program reflect the diversity of
Bioinformatics as a research field as they include genomics and proteomics (Andrade,
Drouin, Golshani, Stintzi, Xia), genome evolution and systems biology (Andrade, ArisBrosou, Drouin, Dumontier, Sankoff, Xia), modeling and statistical analysis (ArisBrosou, Pestov, Gorelick) and database design and algorithms (Bertossi, Dehne,
Kranakis, Sankoff, Turcotte).
Faculty Name & Rank
M/F
Ret.
Date
Home Unit
Supervisory
privileges
Andrade, Miguel – CRC Tier 2
M
NA
CMM (UO)
Full
Aris-Brosou, Stéphane – Assistant M
NA
Biology - OCIB (UO)
Full
Baetz, Kristin – Assistant
F
NA
BMI (UO)
Full
Bertossi, Leopoldo – Professor
M
NA
SCS – OCICS (CU)
Full
Cheetham, James – Professor
M
NA
Biology - OCIB (CU)
Full
Dehne, Frank – Professor
M
NA
SCS– OCICS (CU)
Full
Drouin, Guy – Professor
M
NA
Biology - OCIB (UO)
Full
Dumontier, Michel – Assistant
M
NA
Full
Figeys, Daniel – Professor
M
NA
Biology - OCIB / SCS OCICS
BMI (UO)
Golshani, Ashkan – Assistant
M
NA
Biology – OCIB (CU)
Full
Gorelick, Root – Assistant
M
NA
Full
Kaerns, Mads – Assistant
M
NA
Biology – OCIB/OCIMS
(CU)
CMM (UO)
Kranakis, Evangelos – Professor
M
NA
SCS – OCICS (CU)
Full
Pestov, Vladimir – Professor
M
NA
MS - OCIMS (UO)
Full
Sankoff, David – CRC Tier 1
M
NA
MS - OCIMS (UO)
Full
Sinha, Sanjoy - Assistant
M
NA
MS – OCIMS (CU)
Full
Stintzi, Alain – Associate
M
NA
BMI (UO)
Full
Turcotte, Marcel – Assistant
M
NA
SITE – OCICS (UO)
Full
Xia, Xuhua – Associate
M
NA
Biology – OCIB (UO)
Full
TBA(1) – Assistant
Full
Full
BMI / CMM (UO)
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NOTES — (1) The Faculty of Medicine (BMI/CMM programs) is still recruiting candidates who may want to join the
program. Abbreviations: Biology: Department of Biology; BMI: Department of Biochemistry, Microbiology and
Immunology at the University of Ottawa; CMM: Department of Cellular and Molecular Medicine at the University of
Ottawa; CRC: Canada Research Chair; MS: Department of Mathematics and Statistics; OCIB: Ottawa-Carleton
Institute of Biology; OCIBME: Ottawa-Carleton Institute of Biomedical Engineering; OCICS: Ottawa-Carleton
Institute of Computer Science; OCIMS: Ottawa-Carleton Institute of Mathematics and Statistics; OHRI: Ottawa
Health Research Institute; SITE: School of Information Technology and Engineering; NA: not applicable.
5) Governance
i)
Structure and roles
The collaborative program will be governed by a Coordinator, an Associate
Coordinator, a Coordinating Committee. The function and role of each are defined as
follows:
Coordinator
- Serve as primary point of contact for the collaborative program.
- Responsible for marketing and promotion of the program.
- Act as chair of the Coordinating Committee.
- Inform applicants of the Coordinating Committee decisions.
Associate Coordinator
- Act as Coordinator when the coordinator is not available.
- Prepare applications for consideration by the Coordinating Committee.
- Take minutes of Coordinating Committee meetings.
- Aid in the administration of the Collaborative Program.
Coordinating Committee
- Vote on the admission of students into the collaborative program.
- Vote on the granting of the specialization to a graduating student.
- Review and assess admission policies and their implementation within the
collaborative program.
- Recommend course creation, abolition or modifications.
- Review suggestions and/or complaints from professors or students about
courses/curricula.
- Review suggestions for nomination to membership in the core faculty.
- Oversee program reviews and appraisals.
Graduate Student Committee
Composed entirely of graduate students, the graduate student committee will serve as a
liaison between the graduate students and the core faculty. It will also help to gather
and disseminate information of interest to graduate students entering the collaborative
program (courses, scholarships, career opportunities, etc.).
ii)
Membership
Coordinator/Associate Coordinator
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Both the Coordinator and the Associate Coordinator will be elected for a two-year term,
selected from members of the Coordinating Committee. The roles of coordinator and
associate coordinator will alternate between the two universities. The Associate
Coordinator may replace the Coordinator at the end of his/her term, and is subject to
confirmation by the Coordination Committee. Elections to select a new Coordinator or
Associate Coordinator will take place every two (2) years.
Coordinating Committee
The Coordinating Committee will consist of core faculty members of the collaborative
program. Ten core faculty members, five from each university will be elected for four
years. Elections will be held among core faculty members. In order to have a rolling
renewal of committee members, elections will take place every other year to renew half
the members. The Coordinating Committee will meet at least twice a year to process
program applications.
Members of the Collaborative Program
Any member of a participating unit may be eligible for membership in the collaborative
program. The list of members of the Collaborative Program will be updated at least
once a year by the Coordinating Committee. Nominations will be forwarded to the
Coordinator, and voted electronically or at the next Committee meeting. Nomination
criteria will include graduate supervisory privilege by their respective Faculty of
Graduate Studies (FGS-FGPS), ongoing research in Bioinformatics and recent
publications (within the last five years).
6) Courses related to collaborative program
The following non-exclusive set of courses is recommended for applicants seeking to
augment foundational or Bioinformatics knowledge above and beyond the collaborative
program requirements (section 3iiiA) while fulfilling their unit requirements. Course
offerings vary from year to year; a complete listing is available from the FGPS.
Courses with three-letter codes are given at the University of Ottawa while those with
four-letter course codes are given at Carleton University. A student may enroll and
obtain credit for any graduate course offered by either university. Unless otherwise
noted, each course is worth three credits at the University of Ottawa or the equivalent
half-credit at Carleton University.
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BCH 8102 SELECTED TOPICS IN PROTEIN STRUCTURE AND FUNCTION
BCH 8108 ADVANCED METHODS OF MACROMOLECULAR STRUCTURE
DETERMINATION
BIO 5207 (BIOL 5500) SELECTED TOPICS (1 credit CU / 6 credit UO)
BIO 5302 (BIOL 5105) METHODS IN MOLECULAR GENETICS
BIO 5306 (BIOL 5409) MATHEMATICAL MODELING FOR BIOLOGISTS
BIO 8100 (BIOL 5501) SELECTED TOPICS IN BIOLOGY I
BIO 8102 (BIOL 5502) SELECTED TOPICS IN BIOLOGY II
BIO 8301 (BIOL 5201) EVOLUTIONARY GENETICS AND COMPUTER
ANALYSES
CMM 5304 INTRODUCTION TO DEVELOPMENTAL BIOLOGY
CMM 8104 CELL GROWTH AND DEVELOPMENTAL BIOLOGY
CMM 8310 CURRENT TOPICS IN RNA MOLECULAR BIOLOGY
COMP 5105 (CSI 5132) PARALLEL PROCESSING SYSTEMS
COMP 5306 (CSI 5100) DATA INTEGRATION
COMP 5307 (CSI 5101) KNOWLEDGE REPRESENTATION
CSI 5126 (COMP 5108) ALGORITHMS IN BIOINFORMATICS
CSI 5163 (COMP 5703) ALGORITHM ANALYSIS AND DESIGN
CSI 5165 (COMP 5709) COMBINATORIAL ALGORITHMS
CSI 5387 (COMP 5706) DATA MINING AND CONCEPT LEARNING
CSI 5526 (COMP 5180) ALGORITHMES EN BIOINFORMATIQUE
CSI 5565 (COMP 5709) ALGORITHMES COMBINATOIRES
MAT 5170 (STAT 5708) PROBABILITY THEORY I
MAT 5171 (MATH 5709) PROBABILITY THEORY II
MAT 5181 (STAT 5703) DATA MINING I
MAT 5182 (STAT 5702) MODERN APPLIED / COMPUTATIONAL STATISTICS
MAT 5190 (STAT 5600) MATHEMATICAL STATISTICS I
MAT 5191 (STAT 5501) MATHEMATICAL STATISTICS II
MAT 5198 (STAT 5701) STOCHASTIC MODELS
MAT 5314 (MATH 6508) TOPICS IN PROBABILITY AND STATISTICS
MAT 5319 (MATH 6507) TOPICS IN PROBABILITY AND STATISTICS
MAT 5570 (STAT 5708) THÉORIE DES PROBABILITÉS I
MAT 5571 (STAT 5709) THÉORIE DES PROBABILITÉS II
MAT 5591 (STAT 5501) INFÉRENCE STATISTIQUE
MAT 5598 (MATH 5701) MODÈLES STOCHASTIQUES
SYS 5120 / MAT 4371 APPLIED PROBABILITY
7) Additional information
i)
Language requirements
Carleton University thesis and examinations will be in English. University of Ottawa
thesis and examinations and theses may be in English or in French. Some courses held
at the University of Ottawa may be offered in both English and French.
ii)
Location of the Bioinformatics courses
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The program courses will be given on the main campus of the University of Ottawa.
The Bioinformatics seminar will be given at Carleton University.
iii)
Fast-tracking to PhD programs
Students of the Collaborative Program who decide to transfer to a PhD program
without completing their Masters’ degree will not be eligible for the “Specialization in
Bioinformatics” designation on their diploma.
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Course Descriptions
BNF 5106 / BIO 5106 / BIOL 5XXX: Bioinformatics
Major concepts and methods of Bioinformatics. Topics may include, but are not limited to:
genetics, statistics & probability theory, alignments, phylogenetics, genomics, data mining, protein
structure, cell simulation and computing. University of Ottawa (3 credits), Carleton University (0.5
credit).
BNF 5506 / BIO 5506 : Bioinformatique
Concepts et méthodes en bioinformatique. Les sujets abordés peuvent inclure, sans être limités à :
génétique, statistiques et théorie des probabilités, alignements, phylogénétique, génomique,
structure de protéines, simulation cellulaire et méthodes numériques. University of Ottawa (3
credits).
BNF 5XXX / BIO 5XXX / BIOL 5XXX: Bioinformatics seminar
Current topics in Bioinformatics. For credit, each student will make a presentation and submit a
written report on their seminar; both must be judged to be satisfactory by the faculty. Student,
faculty and invited seminar speakers. University of Ottawa (3 credits), Carleton University (0.5
credit).
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