Not all courses are offered each academic year. Additional courses may be available.
Please refer to the course calendar for a listing of available classes.
Students should also refer to program requirements to determine which courses are needed to complete your IBBME degree.
This course presents a comprehensive review of the developments occurring in dental biomaterials research, under three main themes:
- Materials Processing and Technologies,
- Material/Biological Interfaces, and
- Clinical Applications and Associated Biomaterial Issues.
There will be no formal reports or exams in this course, however the research ability of the graduate students will be assessed throughout the term based on three criteria:
Ability to identify clinical and/or scientific problems, to propose a viable plan to study the problems, and to be able to defend their plan.
This course discusses the concept of the bone/implant interface by combining the multi disciplinary approach necessary to understand both the material & biological aspects of the interface. All materials currently used in bone implants are treated from a surface science perspective together with the activities of both major types of bone cells; osteoblasts and osteoclasts. The cell biological aspects of the interface are covered within the context of explaining the tissue arrangements found at bone implant surfaces.
This seminar course based on Bio-photonics textbook and recent literature will review the field of Bio-photonics, and the interactions of light and biological matter.
The first part of the course is focused on reviewing the fundamentals of Bio-photonics while the second part will review various applications of Bio-photonics.
It will include topics like: Overview, Interaction of light with matter, Light sources and detectors, Optical microscopy, Cellular imaging, Optical Bio-sensing, Vision, Micro-arrays, Photodynamic therapy, and Optical Coherence tomography.
This course covers the application of electrical engineering techniques to the study of the human senses. More and more engineers find it important to include the human user as part of the design process, hence the need for a proper understanding of the human perceptual process. Examples include multimedia, human-computer interaction and medical devices. We will cover the application of information theory and signal detection theory to the study of the human senses. Other topics include sensorineural engineering, the measurement of human performance, as well as an introduction to the requisite physiology and psychology. Course work will involve a research project and a final examination.
NOTE: This course is offered by the Department of Electrical and Computer Engineering. Please contact ECE for any course or registration information.
The senses from the point of view of an engineer. This course explores the theoretical foundations of the senses from both a systems and a neurophysiological point of view. Emphasis will be placed on understanding the senses holistically rather than individually (i.e. we study the common features that span the various sensory modalities). The course material will involve the application of ideas drawn from information theory, statistical signal detection theory and probability theory. In particular, we cover the following theories: (1) the signal detection approach to sensory analysis (vis-à-vis Donald Laming’s theory of differential coupling), the information encoded by sensory neurons, generalized Fechnerian psychophysics (e.g. the entropy theory of Kenneth Norwich), and finally the probabilistic approach to perception.
Along the way, concepts crucial to the study of sensory system are also introduced including: the identification and categorization of sensory stimuli, reaction time, decision-making processes, differentiation of stimuli, the limits of perceptibility, and large-scale integration of sensory information. The course will also consider applications of sensory research to pattern recognition, multimedia and biological computers. Course work will involve surveying the existing literature, doing a research project in small groups and a final examination. No biology background is required although some familiarity with the concept of probability is preferred.
(Students who took the course Sensory Cybernetics and the Theoretical Foundation of the Senses will not be allowed to take this course under the new title.)
This course will focus on the mechanisms associated with the assembly of molecular and biomolecular systems, including colloids, small molecule organic crystals, and protein complexes.
The goal of the course is to foster an understanding of the subtle interactions that influence the process of assembly, which has wide ranging implications in fields ranging from materials science to structural biology.
Examples will be drawn from the current literature encompassing studies of self-assembly in solution, at surfaces, and into the solid state. Supplementary reading and a term project targeting some aspect of molecular assembly will be assigned.
Professor Richard S.C. Cobbold, (cobbold@ECF.utoronto.ca, Room MB316A)
Following a brief historical review, wave propagation from simple structures is examined with the help of the Rayleigh-Sommerfeld diffraction equations. The Rayleigh integral is obtained and applied for determining both the transient and steady-state radiation characteristics from a variety of sources. The theory of ultrasound scattering is developed and applied for understanding scattering by soft tissue, including blood. This is followed by the design and characterization of transmitting and receiving transducers. Included, is a consideration of materials, models and methods for experimental evaluation of performance. The design and properties of B-mode imaging arrays are described along with their practical application. Doppler ultrasound for flow assessment and flow imaging, spectral analysis of Doppler signals and related methods are also described.
The course follows much of the material in:
Cobbold, R.S.C., Foundations of Biomedical Ultrasound, Oxford Univ. Press, New York, 2007 (approx. $100 US).
Those attending the course are provided with a key to download much of the book material together with related course material. There will be 5 problem assignments throughout the term weighted 50% of the final course mark: the remaining 50% will be based on a 1/2 hour oral exam at the end of the term.
We will present an elementary introduction to the revolutionary and important new theory of Compressed Sensing. We will fill in the basic mathematical prerequisites on Fourier Transforms and Wavelets. Other topics will depend on the interests of the class: we will choose between a detailed explanation of how MRI works, imaging electric properties of tissue, or present modern techniques in signal processing for denoising, segmentation and registration.
General perspective of neural engineering and neurobiology; biological neural networks; parametric neural models using rate processes; nonparametric neural models, using the Volterra-Wiener approach; artificial neural networks as nonparametric neural models.
Physical acoustics, acoustic measurements, electroacoustic transducers, and physiological acoustics. Speech processing, speech recognition algorithms, and signal processing by the auditory system.
Engineering aspects of acoustic design. Electrical models of acoustic systems. Noise, noise-induced hearing loss, and noise control. Introduction to vision and other modalities. Musical and psychoacoustics.
This course, or the equivalent, must normally be taken by all graduate students with a physical science background in the first year of their graduate studies. Basic concepts of Human Physiology taught from a bioengineering viewpoint. This is a course that is specifically designed for graduate students with a physical sciences background. Anti-requisites: BME 350, MIE 331, PSL 201, PSL 301 or other similar courses a determined by the instructor.
This course incorporates lectures and laboratories from other courses, which may be supplemented by reading, lab assignments, and special lectures. Approval by the course Coordinator is required.
This course consists of course(s) in core engineering subjects, and enrichment arranged with course Coordinator. Graduate students wishing to register for this course should see Professor Dolan as soon as possible after September 1. The enrichment may be a project, report, or major laboratory exercise.
Prerequisites: Mathematics at second-year undergraduate level (calculus complex variables, transforms); some background in physics.
This course, offered jointly through IBBME and the Department of Materials Science & Engineering (MSE), covers fundamental aspects of the formation, structure, and properties of natural materials, and the use of derived biological principles such as self-assembly to design synthetic materials for a variety of applications.
Examples are drawn from both structural and functional biomaterials, with emphasis on hybrid systems in which protein-mineral interactions play a key role, such as mineralized tissues and biological adhesives.
Additional materials with remarkable mechanical, optical, and surface properties will be discussed.
Advanced experimental methods for characterizing interfacial biological structures will be highlighted, along with materials synthesis strategies, and structure-property relationships in both biological and engineered materials.
** A required course of the Collaborative Program in Proteomics and Bioinformatics **
This is an integrative graduate level course focused on interactive lectures by invited expert lecturers with open classroom discussions regarding practical aspects of an interdisciplinary approach to proteomics, functional genomics and bioinformatics. It is offered within the academic component of the Collaborative Graduate Program in Genome Biology and Bioinformatics (CPGBB) and satisfies a part of the program’s requirements.
The course is designed to expose graduate students with an interest in proteomics, functional genomics and computational biology – either well developed or just starting—to the “state-of-the-art” in terms of theoretical concepts and real life practical applications and to relate this research back to a student’s own thesis project.
Class discussions will center on the opportunities, challenges and judicious choices of advanced high-resolution experimental and computational methods of proteomics, functional genomics and bioinformatics as applied to genome-scale biology. Students will develop practical skills in writing and evaluating formal research proposals.
This course satisfies one of two course requirements for student enrolled in the Collaborative Graduate Program in Genome Biology and Bioinformatics.
As well, credit can be applied towards the Ph.D. program course requirements in the participating departments.
Due to the interactive nature of this course, the number of places is limited. All student members of the CPGBB and eligible students who have applied to the program will be placed. Enrolment by other students as well as audition of this course requires approval by the program director.
To ensure priority enrolment, please submit a brief outline (in 1-2 paragraphs) indicating your current lab and research interests, why you would like to take this course and what you hope to learn. Send the email to the course coordinator: firstname.lastname@example.org.
A course for the fulfilment of program requirements of the Collaborative Program in Genome Biology and Bioinformatics.
It can be argued that all of post-genomic life-science requires a bioinformatics component. Most of us use some Web-based resources to that end. But the Web-based paradigm of bioinformatics is not well suited
to support multiple queries based on lists of genes, to rerun queries at specific times, as databases grow to integrate information from various sources and to integrate results into the workflow of wet-lab scientific inquiry.
This is increasingly becoming a limiting factor in the lab. Fortunately modern scripting languages such as Perl, on UNIX based computers have matured to a point where it is reasonable for wet-lab scientist to acquire the fundamentals of constructing their own, integrated processes and build on these as their requirements change.
JTB2020 is designed to do just that. It is offered within the academic program of The Collaborative Graduate Program in Genome Biology and Bioinformatics and satisfies a part of the program’s requirements. Significant computer and programming skills are not a course requirement, rather the course aims to teach and train the necessary fundamentals. A basic understanding of bioinformatics concepts, databases and procedures is a prerequisite; JTB2020 is not an overview course but intended to help applying bioinformatics concepts to our students’ own research. Our students will learn what are appropriate objectives for the bioinformatics components of their projects, what strategies can be applied, what they can realistically achieve by themselves, for what they will need help and how to go about getting it.
In this course, we will analyze the re-implementation of a complex bioinformatics procedure for the functional annotation of genes through data integration. We will define a useful platform though which to implement the procedure or a part thereof. Then we will design an implementation and prototype it.
The detailed topics will depend on the needs and interests of the participants, a rough guide is following list:
- UNIX commands and shell scripts
- Perl and CGI
- Wiki concepts, collaboration, process modeling
- HTML and PHP
- UCSC, GBrowse, DAS, Ensembl, data integration
- BioPerl, ontologies and synonyms
- Classification, dimensionality reduction
- For detailed information, please visit the Course Wiki.
An introductory level 4th year undergraduate or graduate course in bioinformatics or computational biology is a course prerequisite. The following courses can be applied towards this requirement:
- BCH 441H—Bioinformatics
- BIO 472H1 / JBZ 1473H—Computational Genomics and Bioinformatics
- MBP 1011H—Foundations of Bioinformatics
Other courses or prior experience can be approved by the course coordinator.
An introduction to the various sciences underlying the use of materials in medicine (i.e. biomaterials) with particular emphasis on the interface between biological media and synthetic tissues. Instructors come from a variety of Graduate Departments and Institutes including Chemical Engineering and Applied Chemistry, Materials Science & Engineering, Biomedical Engineering, Dentistry and Pathology. Additional lectures may be provided by individuals from other universities (e.g. McMaster University). Topics to be covered include: surface physics and analysis, principles of protein adsorption and cell growth on materials, structure and function of key tissues (bone, blood, etc.), principles of tissue responses to biomaterial implantation (toxicity, foreign body reaction).
Prerequisite: physical science/engineering background with some knowledge of materials science of biomaterials.
The emphasis of this course will be on applying quantitative methods to better understand a wide variety of dynamical processes that occur in living cells. Possible topics will include cytoskeletal mechanics and rearrangement, procession of molecular motor proteins, chromosomal segregation during cell division, dynamic and stochastic gene expression as well as genetic networks, and others. Modern approaches to observing cellular dynamics using single-molecule and live cell imaging techniques will be stressed.