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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 the program specific handbooks on our student resources page to determine which courses are needed to complete your IBBME degree.
All MASc, MHSc and PhD students are required to attend a minimum of six graduate student seminars per semester and four invited seminar series talks per year to fulfill BME 1010/1011Y requirements.
Attendance will be taken at all talks using the Top Hat app.
Graduate Student Seminar Series consists of two 25-minute presentations given by graduate students registered in both the BME and the Collaborative Specialization in Biomedical Engineering. Seminars are held every Wednesday, Thursday and Friday, with Distinguished Lectures being held the first Tuesday of every month.
This course provides students exposure to the breadth and depth of research activities in biomedical engineering; assists in the establishment of a biomedical engineering identity within the student population and externally to the University and to funding agencies; provides students with the opportunity of presenting their work in a formal setting, and receiving feedback (on both presentation style and content) prior to their final defence.
The primary goal of the IBBME Graduate Student Seminar Series is to provide practical experience and guidance in the clear, concise oral communication of research results to an audience of educated, though not specialist peers. This is an essential skill for anyone intending to seek a career in scientific research. The emphasis is different from a group-meeting or conference style talk to a specialist audience, but rather on the skills that are important ultimately for job talks or teaching situations.
Another important goal of the series is to provide a broad knowledge of all aspects of research undertaken by other students in IBBME. Attendance at these seminars is a great way to see the broad scope and reach of the graduate program in IBBME
A good, interactive audience is essential to the success of this series—so ask questions. Participation in this series is a core requirement of the IBBME graduate program. Students are expected to attend regularly and anyone failing to attend at less than eight seminars per academic year will be considered as non-participating.
Please be sure to notify your supervisor and supervisory committee members as soon as you are provided with a presentation date so that they can allocate time in their schedules to attend.
Concise abstracts (~ 250 words), including the names of your supervisor and supervisory committee members must be provided prior to your seminar and will be posted to the IBBME website.
Signup for time slots will be sent via email.
This course is open to both MHSc and MEng Students.
This course provides a contemporary sampling of clinical technologies deployed in the continuum of health care.
Recent topics include: MRI physics, guided therapeutics, hemodialysis, clinical information technology, human factors engineering in healthcare, infusion therapy and devices, physiological pressures, laser interaction and medical device tracking.
The course focuses on (1) the scientific principles underlying the clinical instrumentation, (2) the clinical applications of the technologies reviewed, and (3) merits and limitations of current technology.
Lectures are given by faculty and clinical scientists who are experts in their respective areas. All lectures will take place in the teaching hospitals and may include tours of various instrumentation suites, laboratories and patient care areas.
Students are evaluated on the basis of a midterm and a final exam.
This course is open to MHSc in Clinical Engineering students only.
This is a unique course that consists of three components. In the first month, students attend a half-dozen didactic lectures introducing the surgical environment, basic instruments and principles of asepsis.
The initial lecture is given by instructors at the Surgical Skills Centre and includes a group observation of a live surgery with play by play commentary. The remaining lectures are presented by surgeons from the teaching hospitals.
In the second part of the course, students will individually attend a handful of observerships of live surgeries performed by the lecturing surgeons or their counterparts. These observerships typically range from four to eight hours. Students will be required to document a subset of surgeries, focusing particularly on technologies deployed, underlying scientific principles, their limitations, surgical workflow and ideas/designs for improvement.
The final part of the course consists of a research project where each student will write a short paper on an engineering topic related to surgery. At the end of the course, students present their projects before an interdisciplinary panel of academic clinical engineers and surgeons.
This course is open to both MHSc and MEng Students.
This course continues from BME 1405—Clinical Engineering Instrumentation I and provides a contemporary sampling of clinical technologies deployed in the continuum of health care.
Recent topics include: electrosurgery, metabolic measurement technology, magnetoencephalography (MEG) imaging, patient safety, radiotherapy, CT imaging, whole blood analysis, anesthesia technology and rehabilitation technologies.
The course focuses on (1) the scientific principles underlying the clinical instrumentation, (2) the clinical applications of the technologies reviewed, and (3) merits and limitations of current technology. Lectures are given by faculty and clinical scientists who are experts in their respective areas.
All lectures will take place in the teaching hospitals and may include tours of various instrumentation suites, laboratories or patient care areas. Students are evaluated on the basis of a midterm and a final exam.
This course integrates relevant aspects of physiology, pathology, developmental biology, disease treatment, tissue engineering and biomedical devices.
The first part of the course will stress basic principles in each of these disciplines.
The second portion of the course will integrate these disciplines in the context of specific organ systems.
For example, the physiology of the cardiovascular system, the development of the system, cardiovascular disease, the relationship between developmental defects and adult disease, current disease treatment, cardiovascular devices, and the current progress in cardiovascular tissue engineering will be presented.
The teaching material will be gathered from various textbooks and scientific journals.
Whenever possible, experts in the relevant field will teach guest lectures.
This integrative approach will be reflected by a problem-based learning approach to testing and a written report.
In this course, the integration of nanotechnology with biomedical research will be discussed.
The course is broken up into four sections:
- Properties of materials in the nanometer-scale and their integration with biological systems
- Fundamental mechanisms of nanostructure assembly for the build-up of biomedical devices
- Tools and systems for the analysis and characterization of nanoscale materials
- Current biomedical applications of nanomaterials
Protein engineering has advanced significantly with the emergence of new chemical and genetic approaches.
These approaches have allowed the modification and recombination of existing proteins to produce novel enzymes with industrial applications and furthermore, they have revealed the mechanisms of protein function.
In this course, we will describe the fundamental concepts of engineering proteins with biological applications.
A background in molecular biology is recommended.
Fluorescence microscopy and associated biophysical methods are integral to many areas of biological research including biomedical engineering, cell biology, and molecular biology.
This course covers the theory, mechanics, and application of fluorescent microscopy. Students will gain expertise in basic and advanced quantitative fluorescence microscopy in the context of working with living samples.
The course topics include sample preparation (immunofluorescence-, dye-, and fluorescent protein-labeling), multidimensional imaging, confocal microscopy, two-photon microscopy and other advanced imaging techniques.
The course will also cover the associated biophysical methods used to probe live cell dynamics such as fluorescence recovery after photobleaching (FRAP), Förster resonance energy transfer (FRET), and fluorescence correlation spectroscopy (FCS).
By centering on applications to living samples, students with gain the theoretical background and practical knowledge to design and implement live cell imaging experiments.
Students are expected to have a basic knowledge of cell biology.
Image analysis has become a central tool in modern biology.
While the human eye analyze images, its assessments are often qualitative. Computers provide quantitative, unbiased measurements, and enable the automation of the analysis, leading to a larger number of processed samples and a greater power of downstream statistical tests.
In this course, we will discuss the main steps in the analysis of digital images, with an emphasis on different modalities of microscopy data, including confocal, TIRF and super-resolution.
Topics will include image display, filtering, segmentation, mathematical morphology and measurements.
Lectures will be complemented with examples from the current literature.
Students will also have the opportunity to develop solutions to the analysis of images from their own research in a final project.
This graduate level course is intended to provide an in-depth coverage on the theory, practice, and applications of magnetic resonance imaging (MRI).
Topics to be covered include cardiovascular imaging, neuroimaging, body imaging, musculoskeletal imaging, oncological imaging, and cellular and molecular imaging.
The MR imaging techniques, pulse sequences, and contrast agents appropriate to different applications will also be described, in order to equip students with practical knowledge for hands-on work.
The format will be largely based on lectures and literature readings, with invited speakers as appropriate to provide a clinical perspective.
Rehabilitation and biomedical engineering are closely linked in various aspects and need to be studied together. For example, electrical stimulation and robotics technologies have recently been proven to facilitate rehabilitation outcomes. Knowledge of the state-of-the-art engineering technologies is required for students in biomedical engineering research. Furthermore, developing new technologies that assist rehabilitation requires thorough knowledge of physiological systems and understanding how they link to those technologies.
This course will introduce various state-of-the-art technologies in rehabilitation engineering. To cover diverse research topics in the field, expert guest lecturers in each field will be invited. The physiological basis of each technique will be emphasized, to encourage students to understand fundamental principles of each technique and to seek applications in their own areas of research.
Electrical neuromodulation can be defined as the use of electrical nerve stimulation to control the ongoing activity of one or more neural circuits.
This course will cover the fundamental topics related to electrical neuromodulation devices, such as the mammalian nervous system, neural excitation predicted by cable theory, principles of neural recording, long-term performance of implanted devices, and advanced techniques for controlling nervous tissue activation.
The class will also cover selected literature of important clinical applications of electrical neuromodulation, where each student will present and lead the discussion of assigned paper(s).
Finally, there will be group projects (typically consisting of two students) in which students will be provided a choice of topics to investigate under the guidance of the instructor or graduate student(s).
The project may involve the design and testing of novel methods of nerve stimulation/recording or it may involve the implementation of neural circuits using computer software (e.g. neuron).
Neural signals can be used to diagnose diseases, to investigate the mechanisms by which the nervous system operates, and to control assistive devices.
This course will introduce students to state-of-the-art methods in measuring the electrical activity of the nervous system.
The biophysical basis of bioelectric recordings will be described, after which data collection and signal processing methods will be discussed for a range of modalities, including: electroencephalography, intracranial recordings, electromyography, electroneurography, and evoked potentials.
Applications and examples will be provided for each of the techniques studied, drawn from fields including neuroscience, neurorehabilitation, kinesiology, and neurosurgery.
Students will have the opportunity to apply selected methods of the course to a problem in their own areas of research.
This course aims to provide students with practical research and academic skills by:
- Practicing fundamental research questioning, hypothesis generation, and research goals to define an individual research approach
- Exploring project management and research planning to increase individual productivity
- Comprehending the philosophy of research and ethical considerations pertaining to biomedical engineering in order to produce high quality research
- Disseminating individual work in written and oral formats to translate individual knowledge and to share multidisciplinary research in creative ways
To achieve these aims, aspects of academic communication will be practiced through interactive workshops that cover literature searching, proposal writing, peer review, the visual display of information, and knowledge mobilization/translation. Throughout the semester, independent study will be centred on the student’s own research topic with written, oral, and graphical communication; while team work will explore an multi-disciplinary project that encourages the translation of scientific knowledge to broader audiences. Students will develop these skills while learning how to position themselves and their research for employment purposes.
Please note that this course is for research program students only and is not suitable for students in course-based MEng programs.
Today’s biomedical engineers will encounter many situations where an ability to perform basic computer programming is desirable if not essential. This is a hands-on course, teaching graduate students the basics of coding in the context of different biomedical engineering scenarios. Students will become familiar with the UNIX operating environment, Python scripting, and task automation, in addition to analyzing, modelling, and manipulating data. The class will involve working through practical examples and solving real problems through a mix of online and live workshops. This course requires no previous programming experience.
This course (BME1479) is intended to provide students interested in biomedical research with an introduction to core statistical concepts and methods, including experimental design. The course also provides a good foundation in the use of discovery tools provided by a data analysis and visualization software. The topics covered will include: i) Importance of being uncertain; ii) Error bars; iii) Significance, p-values and t-tests; iv) Power and sample size; v) Visualizing samples with box plots; vi) Comparing samples; vii) Non parametric tests; viii) Designing comparative experiments; ix) Analysis of variance and blocking; x) Replication; xi) Two-factor designs; xii) Association, correlation and causation; xiii) Simple linear regression; xiv) Regression diagnostics. The concepts will be illustrated with realistic examples that are commonly encountered by biomedical researchers (as opposed to the simpler examples described in entry-level textbooks). The statistical softwares used in this course are JMP and R Studio.
In this course, students will learn to apply statistical approaches to efficiently design and analyze bioengineering experiments.
The course first briefly reviews some fundamental statistical concepts related to design and analysis of experiments (statistical distributions, the central limit theorem, linear functions of random variables and error propagation, ANOVA, multiple regression).
The main topics covered include: screening designs, full factorial designs, blocking and replication, response surface methods, custom designs, sequential design strategies, non-normal responses and transformations.
The students will learn to apply these statistical approaches to solve practical problems in bioengineering, in particular to examine and control the interactions of living systems with molecular and physical factors. They will also be expected to become proficient in the use of statistical software to design experiments and analyze them.
Finally, students will be expected to gain enough knowledge about experimental design strategies to be able to critically analyze the current scientific literature.
This course is open to MEng in Biomedical Engineering students only.
The overarching goal of this course is to be able to understand the fundamental theories behind the development of biomedical products from idea to commercial release.
At the conclusion of this course, the students should be able to:
- Understand the theory behind the development of biomedical products from idea to commercial release
- Apply the theory to critically analyze the relevant processes
- Integrate the above knowledge with real world examples and solve practical problems
- Deliver projects in a team through interactions and group projects
- Appreciate the translational link between the fundamental concepts of biomedical engineering knowledge and its practical application in the development of commercial medical products, the processing of such products and the design considerations for clinical use of such products
This is a survey course that covers development of biomedical products from idea to commercial release.
The main themes of the course are:
- developing proper requirements
- design control
- regulatory requirements
- IEC 60601 Medical Device standard
- risk management (ISO 14971)
- verification and validation
The course will emphasize fundamental engineering principles that will allow students the ability to become productive team members and give them the background necessary to assume leadership roles in product development. Guest experts, case studies, and real world examples augment the learning experience.
Each theme incorporates fundamental engineering principles that will allow you to work effectively in a medical device company or to bring your own product to market.
Familiarity with engineering design principles or equivalency is a significant asset and is expected, but not a requirement.
Undergraduate engineering design experience should be from an accredited engineering school.
Equivalency will be assessed by the course instructor and determined on an individual basis.
BME 1800 is a complementary course to BME 1801 in the IBBME MEng program.
This course is open to MEng in Biomedical Engineering students only.
The objective of this course is to provide students with regulatory body and ethics considerations by which they engineer safe medical device products intended for use as implantable devices or in contact with body tissue and fluids.
A top down approach will be taken where the regulatory path for product approval and associated costs with product development and validation are reviewed for different biomaterials and devices. This path is then assessed in the context of product specific reimbursement, ethics, safety, competitive positioning and regulatory concerns.
Students will be required to use their existing knowledge of biomaterials and devices, and their biocompatibility to frame the questions, challenges and opportunities with a mind to re-engineering products in order to capitalize on niche regulatory pathways.
The resulting regulatory path gives a good idea of the kind of trial design the product must prevail in and ultimately the design characteristics of the device itself. Decision making will be made with ethical considerations.
The discussion model will focus mostly on the United States regulatory office with some comments on Canada and Europe. Lastly, quantitative product development risks estimates are considered in choosing a product path strategy for proof of concept and approval of safe products.
Ethical issues can also impact design since in biomedical engineering they are currently studied in the fields of bioethics, medical ethics and engineering ethics. Yet, professional ethical issues in biomedical engineering are often different from the ones traditionally discussed in these fields as they need to align with the engineering profession.
Biomedical engineers differ from medical practitioners, and are similar to other engineers, in that they are involved in research for and development of new technology, and do not engage in the study, diagnosis and treatment of patients.
Biomedical engineers differ from other engineers, and are similar to medical practitioners, in that they aim to contribute to good patient care and healthcare.
The ethical responsibilities of biomedical engineers thus combine those of engineers and medical professionals, including a responsibility to adhere to general ethical standards in research and development of technology and to do R&D that adheres to the specific standards set forth by medical ethics and bioethics.
This course focuses on products currently for sale as case studies, or may be approved for sale within the next two years consistent with its practical commercial focus.
MSE 352—Biomaterials and Biocompatibility or equivalent.
Equivalency will be assessed by the course instructor and determined on an individual basis.
The BME 1801 course is a parallel course to the BME 460 course taught to Engineering Science students, and the students will take several courses together. However, BME 1801 students will have their own group project teams.
This course will apply human factors engineering principles to the design of medical devices.
Testing medical devices in a health care setting, with realistic users, will be emphasized to understand why devices fail to perform adequately.
Students in this course will work in teams to complete an evaluation of a medical device design, existing prototype, or commercial product by conducting usability studies, with realistic users, to uncover use errors.
Human factors engineering analysis will be used to propose and make design changes to improve the design and validation testing will be used to prove that design modifications yield a reduction in use-related errors.
Throughout the course, topics will be covered as they relate to applicable medical device industry standards (e.g., quality and risk management of medical devices and usability and human factors engineering of medical devices) through lecture activities, examples, case studies, and the overarching design project.
This course is open to MEng in Biomedical Engineering students only.
This internship is typically undertaken during the summer session and ideally, students should carry out a project in industry, in private consulting firms, hospitals or government institutions.
Students will be expected to cover four important aspects of biomedical device development during their internship:
- Clinical, medical or health needs assessment (need of healthcare providers and patients). For this project component, the students will apply concepts mainly related to their Biomedical Science courses.
- Concept development (literature and patent searches, input from experts). For this project component, the students will apply concepts related to their Engineering, Entrepreneurship, Biomedical Science courses.
- Design and prototyping. For this project component, the students will apply concepts mostly related to their Engineering and Biomedical Sciences courses.
- Development of business models. For this project component, the students will apply concepts mostly related to their Entrepreneurship courses.
The internship will be evaluated by both the internship supervisor and the program director.
This course is for MHSc Clinical Engineering student only.
Clinical Engineering practice is the management of modern health-care technology.
This course provides practical experience in the practice of clinical engineering. Students will gain knowledge and experience in areas such as in-service education, departmental management, equipment acquisition, equipment control, equipment design, facility planning, information systems, regulatory affairs, safety program, system analysis and technology assessment/evaluation.
Students are required to complete 1,250 hours of internships, in two or three separate internships in locations such as health-care facilities, the medical device industry, or health-care consulting firms.
Evaluations are based on bi-weekly activity reports, final written reports and supervisor evaluations.
(note: This course was previously named "BME1454—Regenerative Medicine: Fundamentals & Applications")
This course focuses on regenerative medicine – tissue engineering, stem cells, endogenous repair, gene therapy, - and related topics, as seen through the patent literature. A different patent or patent application is discussed each 2-hour period [Wednesdays at noon, BA2139, Fridays at 9, RS412] to illustrate an aspect of regenerative medicine. Most of the course content will be student presentations. The plan is to have no final exam.
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.
The course deals with the modeling and simulation of physical systems.
It introduces the fundamental techniques to generate and solve the equations of a static or dynamic system. Special attention is devoted to complexity issues and to model order reduction methods, presented as a systematic way to simulate highly-complex systems with acceptable computational cost. Examples from multiple disciplines are considered, including electrical/electromagnetic engineering, structural mechanics, fluid-dynamics. Students are encouraged to work on a project related to
their own research interests.
This seminar course based on Bio-photonics textbooks 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.
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.
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.
Frances Skinner (Physiology)
Milad Lankarany (IBBME)
Computational Neuroscience seeks to understand the fundamental principles of neural dynamics, and how the brain and nervous systems compute. This highly interdisciplinary field requires both experiment and theory and encompasses several disciplines that include physiology, mathematics and engineering. This course will provide a brief background of neurobiological and mathematical concepts, describe the theory and ideas that underlie the models, analyses and methods used in the field today (e.g., Hodgkin-Huxley models, neural coding, oscillations). In addition, the course will provide an overview of the most recent approaches and applications of computational neuroscience in the fields of biomedicine.
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 course for the fulfilment of program requirements of the Collaborative Program in Genome Biology 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: email@example.com.
This course will be cancelled as of Fall 2020
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.
There are six courses that are part of the undergraduate biomedical engineering (BME) minor. Students must fulfill 3.0 credits from the following courses to have the BME minor included in their official transcript.
Prerequisites (one of the following): CHE 353—Engineering Biology, BME 205—Biomolecules & Cells or MIE 100—Dynamics
An introduction to the principles of human body movement.
Specific topics include the dynamics of human motion and the neural motor system, with a focus on the positive/negative adaptability of the motor system.
Students will experience basic techniques of capturing and analyzing human motion. Engineering applications and the field of rehabilitation engineering will be emphasized using other experimental materials.
This course is designed for senior undergraduate and graduate students.
Prerequisite: CHE 353—Engineering Biology
An introduction to the principles of fundamental technologies used in biomedical engineering research, including, but not limited, to tissue culture, protein assays or colourimetric enzymatic-based assays, spectroscopy, fluorescence microscopy, PCR, electrophoresis, DNA manipulation and transfection. These technologies enable the investigation of a wide range of research questions with important clinical implications.
The main focus of the course is to learn about these technologies while subsequent application within the lab will allow evidence-based investigation into specific research questions.
Scientific literature (both good and bad) pertaining to each technology will be reviewed as examples of conducting investigations.
Prerequisite: N/A, but approval to register must be obtained from the IBBME associate director of undergraduate programs
In this project-based design course, teams of students from disciplines across the Faculty of Applied Science & Engineering (enrolled in the biomedical engineering minor) will engage in the bio-medical technology design process to identify, invent and implement a solution to a unmet clinical need
Students will learn about medical technology development and will engage in the process through lectures, guest talks delivered by medical technology experts, hands-on practicums and a student driven design project.
Approval to register in the course must be obtained from the IBBME associate director of undergraduate programs.
Prerequisite: CHE 353—Engineering Biology; approval to register must be obtained from the IBBME associate director of undergraduate programs
Co-requisite: MIE 331—Physiological Control Systems
This course provides students with the opportunity to gain hands-on exposure and experience in dynamic biomedical research laboratories.
Students will be required to perform two modules: one is completed in the fall semester while the second is completed in the winter semester. Each module will provide at minimum 90 hours of hands-on activity.
Students will select opportunities with faculty in laboratories classified within two of three different research themes at the Institute of Biomaterials and Biomedical Engineering (IBBME).
Activities will provide exposure to experimental design, the use of analytical equipment and assessment of relevant literature (scientific, patent and regulatory) related to the research topic identified by the faculty member.
Using a quantitative, problem solving approach, this course will introduce basic concepts in cell biology and physiology. Various engineering modelling tools will be used to investigate aspects of cell growth and metabolism, transport across cell membranes, protein structure, homeostasis, nerve conduction and mechanical forces in biology.
Prerequisite: CHE 353—Engineering Biology
The purpose of this course is to provide undergraduate engineering students with an introduction to physiological concepts and selected physiological control systems present in the human body.
Due to the scope and complexity of this field, this course will not cover all physiological control systems but rather a selected few such as the neuromuscular, cardiovascular, and endocrine control systems.
This course will also provide an introduction to the structures and mechanisms responsible for the proper functioning of these systems. In addition, it will combine linear control theory, physiology and neuroscience with the objective of explaining how these complex systems operate in a healthy human body.
The first part of the course will provide an introduction into physiology and give an overview of the main physiological systems.
The second part of the course will focus on the endocrine system and its subsystems, including glucose regulation, thyroid metabolic hormones and the menstrual cycle.
The third part of the course will include discussion on the cardiovascular system and related aspects such as cardiac output, venous return, control of blood flow by the tissues and nervous regulation of circulation.
The fourth and final section of the course will focus on the central nervous system, the musculoskeletal system, proprioception, kinaesthetic and control of voluntary motion.
Introduction to the application of the principles of mechanical engineering—principally solid mechanics, fluid mechanics, and dynamics—to living systems.
Topics include cellular mechanics, blood rheology, circulatory mechanics, respiratory mechanics, skeletal mechanics and locomotion.
Applications of these topics to biomimetic and biomechanical design are emphasized through a major, integrative group project.