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Master of Engineering (M.Eng.); Biomedical Engineering (Thesis) — Bioinformatics (45 credits)

Offered by: Biomedical Engineering     Degree: Master of Engineering

Program Requirements

Thesis Courses (24 credits)

Required Courses (3 credits)

  • COMP 616D1 Bioinformatics Seminar (1.5 credits)

    Offered by: Computer Science (Faculty of Science)

    Administered by: Graduate Studies

    Overview

    Computer Science (Sci) : Introduction to current trends in Bioinformatics and closely related fields such as genomics and proteomics.

    Terms: Fall 2014

    Instructors: Michael Trevor Hallett, Mathieu Blanchette (Fall)

    • Restrictions: This seminar is restricted to graduate students in the Bioinformatics Option. Enrolment is limited to 30 students.
    • Note: The seminar will meet for 3 hours every second week over Fall and Winter semesters.
    • Students must register for both COMP 616D1 and COMP 616D2.
    • No credit will be given for this course unless both COMP 616D1 and COMP 616D2 are successfully completed in consecutive terms.
  • COMP 616D2 Bioinformatics Seminar (1.5 credits)

    Offered by: Computer Science (Faculty of Science)

    Administered by: Graduate Studies

    Overview

    Computer Science (Sci) : See COMP 616D1 for description.

    Terms: Winter 2015

    Instructors: Michael Trevor Hallett (Winter)

    • Prerequisite: COMP 616D1.
    • No credit will be given for this course unless both COMP 616D1 and COMP 616D2 are successfully completed in consecutive terms.

Complementary Courses (18 credits)

12 credits of courses which have both biomedical content and content from the physical sciences, engineering, or computer science selected from the following:

  • BIOT 505 Selected Topics in Biotechnology (3 credits)

    Offered by: Biology (Faculty of Science)

    Overview

    Biotechnology : Current methods and recent advances in biological, medical, agricultural and engineering aspects of biotechnology will be described and discussed. An extensive reading list will complement the lecture material.

    Terms: Fall 2014

    Instructors: Elias Georges (Fall)

    • Fall
    • Restriction: U3 students
  • BMDE 501 Selected Topics in Biomedical Engineering (3 credits)

    Offered by: Biomedical Engineering (Faculty of Engineering)

    Overview

    Biomedical Engineering : An overview of how techniques from engineering and the physical sciences are applied to the study of selected physiological systems and biological signals. Using specific biological examples, systems will be studied using: signal or finite-element analysis, system and identification, modelling and simulation, computer control of experiments and data acquisition.

    Terms: Fall 2014

    Instructors: W Robert J Funnell (Fall)

    • (3-0-6)
  • BMDE 502 BME Modelling and Identification (3 credits)

    Offered by: Biomedical Engineering (Faculty of Engineering)

    Overview

    Biomedical Engineering : Methodologies in systems or distributed multidimensional processes. System themes include parametric vs. non-parametric system representations; linear/non-linear; noise, transients and time variation; mapping from continuous to discrete models; and relevant identification approaches in continuous and discrete time formulations.

    Terms: Winter 2015

    Instructors: Henrietta L Galiana, Georgios Mitsis (Winter)

    • (3-0-6)
    • Prerequisites: Undergraduate basic statistics and: either BMDE 519, or Signals and Systems (e.g., ECSE 303 & ECSE 304) or equivalent
  • BMDE 503 Biomedical Instrumentation (3 credits)

    Offered by: Biomedical Engineering (Faculty of Engineering)

    Overview

    Biomedical Engineering : The principles and practice of making biological measurements in the laboratory, including theory of linear systems, data sampling, computer interfaces and electronic circuit design.

    Terms: Fall 2014

    Instructors: Ross Wagner (Fall)

    • (3-0-6)
    • Prerequisite: Experience with differential equations, in particular Laplace Transforms and complex numbers (e.g. MATH 263 or MATH 381 or equivalent) or permission of instructor.
  • BMDE 504 Biomaterials and Bioperformance (3 credits)

    Offered by: Biomedical Engineering (Faculty of Engineering)

    Overview

    Biomedical Engineering : Biological and synthetic biomaterials, medical devices, and the issues related to their bioperformance. The physicochemical characteristics of biomaterials in relation to their biocompatibility and sterilization.

    Terms: Winter 2015

    Instructors: Maryam Tabrizian (Winter)

    • (3-0-6)
    • Restriction: Graduate and final-year undergraduate students from physical, biological and medical science, and engineering
  • BMDE 505 Cell and Tissue Engineering (3 credits)

    Offered by: Biomedical Engineering (Faculty of Engineering)

    Overview

    Biomedical Engineering : Application of the principles of engineering, physical, and biological sciences to modify and create cells and tissues for therapeutic applications will be discussed, as well as the industrial perspective and related ethical issues.

    Terms: Winter 2015

    Instructors: Satya Prakash (Winter)

    • (3-0-6)
    • 1.5 hours lecture/1.5 hours seminar per week
    • Restriction: graduate and final year undergraduate students from physical, biological, and medical science, and engineering.
  • BMDE 506 Molecular Biology Techniques (3 credits)

    Offered by: Biomedical Engineering (Faculty of Engineering)

    Overview

    Biomedical Engineering : Introduction to major techniques of molecular biology for physical scientists.

    Terms: This course is not scheduled for the 2014-2015 academic year.

    Instructors: There are no professors associated with this course for the 2014-2015 academic year.

    • (1-5-3)
    • Prerequisites: MATH 222, BIOL 200 or BIOL 201, CHEM 212 or CHEM 213 or PHYS 253
    • Restrictions: Limited to 18 students. Calculus required, physics or physical chemistry (thermodynamics, statistical mechanics) preferred. Primarily for graduate students or advanced undergraduate students in the physical sciences who are interested in learning molecular biology techniques. Preference given to graduate students in Biomedical Engineering and Physics. Students who have completed BIOC 300 or MIMM 366 are not eligible.
  • BMDE 508 Introduction to Micro and Nano-Bioengineering (3 credits)

    Offered by: Biomedical Engineering (Faculty of Medicine)

    Overview

    Biomedical Engineering : The micro and nanotechnologies that drive and support the miniaturization and parallelization of techniques for life sciences research, including different inventions, designs and engineering approaches that lead to new tools and methods for the life sciences - while transforming them - and help advance our knowledge of life.

    Terms: Fall 2014

    Instructors: David Juncker (Fall)

    • (3-0-6)
    • Prerequisite: Permission of instructor
    • This course is intended for graduate and advanced undergraduate students having a biological/medical background or an engineering, physical sciences background. Engineering students enrolled in the Minor in Biomedical Engineering, or Honours in Electrical Engineering and Honours in Mechanical Engineering, should be particularly interested.
  • BMDE 519 Biomedical Signals and Systems (3 credits)

    Offered by: Biomedical Engineering (Faculty of Engineering)

    Overview

    Biomedical Engineering : An introduction to the theoretical framework, experimental techniques and analysis procedures available for the quantitative analysis of physiological systems and signals. Lectures plus laboratory work using the Biomedical Engineering computer system. Topics include: amplitude and frequency structure of signals, filtering, sampling, correlation functions, time and frequency-domain descriptions of systems.

    Terms: Fall 2014

    Instructors: Robert E Kearney (Fall)

    • (3-0-6)
    • Prerequisites: Satisfactory standing in U3 Honours Physiology; or U3 Major in Physics-Physiology; or U3 Major Physiology-Mathematics; or permission of instructor
  • BMDE 600D1 Seminars in Biomedical Engineering (1.5 credits)

    Offered by: Biomedical Engineering (Faculty of Medicine)

    Administered by: Graduate Studies

    Overview

    Biomedical Engineering : This course requires students to regularly attend the departmental seminar series and to present a seminar related to their research.

    Terms: Fall 2014

    Instructors: Satya Prakash, Adam Hendricks (Fall)

    • Students must register for both BMDE 600D1 and BMDE 600D2.
    • No credit will be given for this course unless both BMDE 600D1 and BMDE 600D2 are successfully completed in consecutive terms
    • Students must register for BMDE 600D1 before BMDE 600D2
    • Restriction(s): This course is open only to students registered in the second term or later of the M.Eng. in Biomedical Engineering (Thesis) and M.Eng. in Biomedical Engineering; (Thesis) Bioinformatics programs.
    • Not open to students who have taken BMDE 500D1/D2.
  • BMDE 600D2 Seminars in Biomedical Engineering (1.5 credits)

    Offered by: Biomedical Engineering (Faculty of Medicine)

    Administered by: Graduate Studies

    Overview

    Biomedical Engineering : This course requires students to regularly attend the departmental seminar series and to present a seminar related to their research.

    Terms: Winter 2015

    Instructors: Satya Prakash, Adam Hendricks (Winter)

    • Students must register for both BMDE 600D1 and BMDE 600D2.
    • No credit will be given for this course unless both BMDE 600D1 and BMDE 600D2 are successfully completed in consecutive terms.
    • Students must register for BMDE 600D1 before BMDE 600D2.
    • Restriction(s): This course is open only to students registered in the second term or later of the M.Eng. in Biomedical Engineering (Thesis) and M.Eng. in Biomedical Engineering; (Thesis) Bioinformatics programs.
    • Not open to students who have taken BMDE 500D1/D2.
  • BMDE 650 Advanced Medical Imaging (3 credits)

    Offered by: Biomedical Engineering (Faculty of Medicine)

    Administered by: Graduate Studies

    Overview

    Biomedical Engineering : Review of advanced techniques in medical imaging including: fast magnetic resonance imaging (MRI), functional MRI, MR angiography and quantitative flow measurement, spiral and dynamic x-ray computed tomography, 2D/3D positron emission tomography (PET), basic PET physiology, tracer kinetics, surgical planning and guidance, functional and anatomical brain mapping, 2D and 3D ultrasound imaging, and medical image processing.

    Terms: Winter 2015

    Instructors: Louis Collins (Winter)

  • BMDE 651 Orthopaedic Engineering (3 credits)

    Offered by: Biomedical Engineering (Faculty of Medicine)

    Administered by: Graduate Studies

    Overview

    Biomedical Engineering : Science and technology related to implants used for various orthopaedic reconstructive procedures, with emphasis on artificial hip and knee joint prostheses.

    Terms: This course is not scheduled for the 2014-2015 academic year.

    Instructors: There are no professors associated with this course for the 2014-2015 academic year.

    • Restriction: Permission of the instructor.
  • COMP 526 Probabilistic Reasoning and AI (3 credits)

    Offered by: Computer Science (Faculty of Science)

    Overview

    Computer Science (Sci) : Belief networks, Utility theory, Markov Decision Processes and Learning Algorithms.

    Terms: This course is not scheduled for the 2014-2015 academic year.

    Instructors: There are no professors associated with this course for the 2014-2015 academic year.

    • 3 hours
    • Prerequisites: COMP 206, COMP 360, COMP 424 and MATH 323
  • COMP 546 Computational Perception (4 credits)

    Offered by: Computer Science (Faculty of Science)

    Overview

    Computer Science (Sci) : Computational models of visual perception and audition. Vision problems include stereopsis, motion, focus, perspective, color. Audition problems include source localization and recognition. Emphasis on physics of image formation, sensory signal processing, neural pathways and computation, psychophysical methods.

    Terms: This course is not scheduled for the 2014-2015 academic year.

    Instructors: There are no professors associated with this course for the 2014-2015 academic year.

    • 3 hours
    • Restrictions: Not open to students who have taken COMP 646.
  • COMP 558 Fundamentals of Computer Vision (3 credits)

    Offered by: Computer Science (Faculty of Science)

    Overview

    Computer Science (Sci) : Biological vision, edge detection, projective geometry and camera modelling, shape from shading and texture, stereo vision, optical flow, motion analysis, object representation, object recognition, graph theoretic methods, high level vision, applications.

    Terms: Winter 2015

    Instructors: Kaleem Siddiqi (Winter)

    • 3 hours
    • Prerequisites: COMP 206, COMP 360, MATH 222, MATH 223
    • Restriction: not open to students who have taken 308-766 before January 2001
  • COMP 761 Advanced Topics Theory 2 (4 credits)

    Offered by: Computer Science (Faculty of Science)

    Administered by: Graduate Studies

    Overview

    Computer Science (Sci) : Advanced topics in theory related to computer science.

    Terms: This course is not scheduled for the 2014-2015 academic year.

    Instructors: There are no professors associated with this course for the 2014-2015 academic year.

  • ECSE 523 Speech Communications (3 credits)

    Offered by: Electrical & Computer Engr (Faculty of Engineering)

    Overview

    Electrical Engineering : Articulatory and acoustic descriptions of speech production, speech production models, speech perception, digital processing of speech signals, vocodors using formant, linear predictive and cepstral techniques, overview of automatic speech recognition systems, speech synthesis systems and speaker verification systems.

    Terms: Winter 2015

    Instructors: Douglas D O'Shaughnessy (Winter)

    • (3-0-6)
    • Prerequisite: ECSE 412 or ECSE 512
  • ECSE 526 Artificial Intelligence (3 credits)

    Offered by: Electrical & Computer Engr (Faculty of Engineering)

    Overview

    Electrical Engineering : Design principles of autonomous agents, agent architectures, machine learning, neural networks, genetic algorithms, and multi-agent collaboration. The course includes a term project that consists of designing and implementing software agents that collaborate and compete in a simulated environment.

    Terms: Winter 2015

    Instructors: Jeremy Cooperstock (Winter)

    • (3-0-6)
    • Prerequisite: ECSE 322
  • ECSE 529 Computer and Biological Vision (3 credits)

    Offered by: Electrical & Computer Engr (Faculty of Engineering)

    Overview

    Electrical Engineering : Vision in man and machine, imaging process, spatial and frequency domain filters, biological vision, edge detection, intermediate features, connecting biological and psychophysical vision, science of colour.

    Terms: Fall 2014

    Instructors: Martin D Levine (Fall)

    • (3-0-6)
    • Prerequisite: ECSE 304 or ECSE 306
  • ECSE 626 Statistical Computer Vision (4 credits)

    Offered by: Electrical & Computer Engr (Faculty of Engineering)

    Administered by: Graduate Studies

    Overview

    Electrical Engineering : An overview of statistical techniques as applied to computer vision and image processing. Topics include regularization, Kalman filtering, Markov-Chain Monte Carlo methods, importance sampling and particle filtering, Markov Random fields, parameter estimation, mean-field techniques, stochastic and deterministic annealing, principal and independent components analysis.

    Terms: Winter 2015

    Instructors: Tal Arbel (Winter)

    • (3-0-9)
    • Prerequisites: ECSE 529 or equivalent, ECSE 305 or equivalent.
  • ECSE 681 Colloquium in Electrical Engineering (4 credits)

    Offered by: Electrical & Computer Engr (Faculty of Engineering)

    Administered by: Graduate Studies

    Overview

    Electrical Engineering : Directed reading, seminar and discussion course in various subjects of current interest in electrical engineering research.

    Terms: Fall 2014

    Instructors: Jeremy Cooperstock (Fall)

  • EXMD 610 Molecular Methods in Medical Research (3 credits)

    Offered by: Medicine (Faculty of Medicine)

    Administered by: Graduate Studies

    Overview

    Experimental Medicine : Different molecular methods used in biomedical research, including chromatography, purification and analysis of proteins and nucleic acids, various techniques in molecular biology, transgenic technology, and stem cells. Lectures, some demonstrations, and short seminars given by the students.

    Terms: Winter 2015

    Instructors: William S Powell, Simon Rousseau (Winter)

  • MDPH 607 Introduction to Medical Imaging (3 credits)

    Offered by: Medical Physics Unit (Faculty of Medicine)

    Administered by: Graduate Studies

    Overview

    Medical Physics : A review of the principles of medical imaging as applied to conventional diagnostic radiography, digital subtraction radiography, computed tomography and magnetic resonance imaging. The course emphasizes a linear system approach to the formation, processing and display of medical images.

    Terms: Winter 2015

    Instructors: Andrew J Reader, Ives Levesque (Winter)

    • Prerequisite: MDPH 615
  • MDPH 611 Medical Electronics (2 credits)

    Offered by: Medical Physics Unit (Faculty of Medicine)

    Administered by: Graduate Studies

    Overview

    Medical Physics : An introductory course on electronics, with emphasis on digital electronics, data acquisition and microprocessors applied to instrumentation. A basic knowledge of electronics is assumed, but the detailed course contents may vary from year to year, depending on the background of the students.

    Terms: Fall 2014

    Instructors: Pierre Leger (Fall)

  • MDPH 612 Computers in Medical Imaging (2 credits)

    Offered by: Medical Physics Unit (Faculty of Medicine)

    Administered by: Graduate Studies

    Overview

    Medical Physics : The role of computers in the acquisition and storage of data in medical imaging systems, with special reference to computed tomography, gamma cameras, positron emission tomography. Special attention is paid to the interfacing requirements of each device and to image display systems. Demonstrations of some of these systems are included.

    Terms: Winter 2015

    Instructors: Horacio J Patrocinio, Francois Deblois (Winter)

    • Prerequisites: MDPH 611 or equivalent, MDPH 614, MDPH 615.
    • Corequisite: MDPH 607.
  • MECH 500 Selected Topics in Mechanical Engineering (3 credits)

    Offered by: Mechanical Engineering (Faculty of Engineering)

    Overview

    Mechanical Engineering : A course to allow the introduction of new topics in Mechanical Engineering as needs arise, by regular and visiting staff.

    Terms: Fall 2014

    Instructors: Yaoyao Zhao (Fall)

    • (3-0-6)
  • MECH 561 Biomechanics of Musculoskeletal Systems (3 credits)

    Offered by: Mechanical Engineering (Faculty of Engineering)

    Overview

    Mechanical Engineering : The musculoskeletal system; general characteristics and classification of tissues and joints. Biomechanics and clinical problems in orthopaedics. Modelling and force analysis of musculoskeletal systems. Passive and active kinematics. Load-deformation properties of passive connective tissue, passive and stimulated muscle response. Experimental approaches, case studies.

    Terms: This course is not scheduled for the 2014-2015 academic year.

    Instructors: There are no professors associated with this course for the 2014-2015 academic year.

    • (3-0-6)
    • Prerequisite (Undergraduate): MECH 321 and (MECH 315 or MECH 419)
  • PHGY 517 Artificial Internal Organs (3 credits)

    Offered by: Physiology (Faculty of Science)

    Overview

    Physiology : Physiological, bioengineering, chemical and clinical aspects of artificial organs including basic principles and physiopathology of organ failure. Examples: oxygenator, cardiac support, vascular substitutes, cardiac pacemaker, biomaterials and tissue engineering, biocompatibility.

    Terms: This course is not scheduled for the 2014-2015 academic year.

    Instructors: There are no professors associated with this course for the 2014-2015 academic year.

    • Winter
    • Prerequisite (Undergraduate): permission of instructors.
  • PHGY 518 Artificial Cells (3 credits)

    Offered by: Physiology (Faculty of Science)

    Overview

    Physiology : Physiology, biotechnology, chemistry and biomedical application of artificial cells, blood substitutes, immobilized enzymes, microorganisms and cells, hemoperfusion, artificial kidneys, and drug delivery systems. PHGY 517 and PHGY 518 when taken together, will give a complete picture of this field. However, the student can select one of these.

    Terms: Fall 2014

    Instructors: Thomas Ming Swi Chang, Satya Prakash (Fall)

    • Fall
    • Prerequisite (Undergraduate): permission of instructors.

6 credits selected from the following courses:

  • BINF 621 Bioinformatics: Molecular Biology (3 credits)

    Offered by: Plant Science (Agricultural & Environmental Sciences)

    Administered by: Graduate Studies

    Overview

    Bioinformatics : The main problems related to the analysis of biological sequences (sequence comparison, homology, gene annotation, phylogenetic inference, comparative genomics) and the computational approaches (dynamic programming algorithms, Blast heuristics, hidden Markov models, Bayesian statistics).

    Terms: Fall 2014

    Instructors: Martina Stromvik (Fall)

    • Restriction: Enrolment by students in the Bioinformatics option or by permission from the course coordinators only. Limited to 30 students.
  • BMDE 652 Bioinformatics: Proteomics (3 credits)

    Offered by: Biomedical Engineering (Faculty of Medicine)

    Administered by: Graduate Studies

    Overview

    Biomedical Engineering : Overview of high-throughput proteomic technologies commonly employed to study the localization and function of all proteins in an organism, and the bioinformatic approaches to analyze raw data and deposit them in proteome databases.

    Terms: This course is not scheduled for the 2014-2015 academic year.

    Instructors: There are no professors associated with this course for the 2014-2015 academic year.

    • Prerequisite: Enrolment in Bioinformatics option program or permission by coordinators.
    • Note: The course is inter-disciplinary and is targeted to students with different scientific backgrounds. A substantial portion of marks will be given based on practical assignments.
  • BTEC 555 Structural Bioinformatics (3 credits)

    Offered by: Parasitology (Agricultural & Environmental Sciences)

    Overview

    Biotechnology : Fundamentals of protein structure and the application of tools for structure determination, how protein structure allows us to understand the complex biological functions, and how knowledge of protein structure can contribute to drug discovery.

    Terms: Winter 2015

    Instructors: Reza Salavati (Winter)

    • Winter
    • 1-hr lecture, followed by 2 hrs of computer lab.
    • Prerequisite: Molecular biology or biochemistry, and basic bioinformatics, or permission of instructor.
  • COMP 618 Bioinformatics: Functional Genomics (3 credits)

    Offered by: Computer Science (Faculty of Science)

    Administered by: Graduate Studies

    Overview

    Computer Science (Sci) : Techniques related to microarrays (normalization, differential expression, class prediction, class discovery), the analysis of non-coding sequence data (identification of transcription factor binding sites), single nucleotide polymorphisms, the inference of biological networks, and integrative Bioinformatics approaches.

    Terms: Winter 2015

    Instructors: Michael Trevor Hallett (Winter)

    • Prerequisite: Enrolment in Bioinformatics Option Program or permission of coordinators.
    • Restrictions: Enrolment by students in the Bioinformatics Option Program or by permission of course coordinators only. Computer Science graduate students not in the Bioinformatics Option Program need additional permission of the M.Sc. or Ph.D. Committee respectively.
  • PHGY 603 Systems Biology and Biophysics (3 credits)

    Offered by: Physiology (Faculty of Medicine)

    Administered by: Graduate Studies

    Overview

    Physiology : Introduction to classical and current topics in biophysics and systems biology in order to model the control of gene expression and intracellular signal transduction, as well as gene spread in populations.

    Terms: This course is not scheduled for the 2014-2015 academic year.

    Instructors: There are no professors associated with this course for the 2014-2015 academic year.

    • Prerequisite: Knowledge of differential equations at the MATH 315 level or equivalent.
    • Notes: Enrolment is limited to 20 students per semester. The course is 1.5 hours of lecture and 1.5 hours of seminar per week. Readings will focus on classic and current journal articles.

In addition, students are required to present their work as a conference paper or departmental seminar before being granted the M.Eng. (Bioinformatics Option) degree.

Faculty of Medicine—2014-2015 (last updated Feb. 18, 2014) (disclaimer)