TORONTO METROPOLITAN UNIVERSITY

Course Outline (W2024)

BME809: Biomedical Systems Modelling

Instructor(s)Dr. Dafna Sussman [Coordinator]
Office:
Phone: (416) 979-5000 x 553767
Email: dafna.sussman@torontomu.ca
Office Hours: Monday 12-1pm By appointment
Calendar DescriptionMathematical modeling of biomedical systems. Lumped and distributed models of electrical, mechanical, and chemical processes applied to cells, tissues, and organ systems.
PrerequisitesBLG 601 and BLG 701 and BME 229 and BME 639
Antirequisites

None

Corerequisites

None

Compulsory Text(s):
  1. Signals and Systems in Biomedical Engineering: Physiological Systems Modeling and Signal Processing (Third Edition), Suresh R. Devasahayam. Springer Singapore, 2019 (ebook ISBN 978-981-13-3531-0, hardcover book ISBN 978-981-13-3530-3)
Reference Text(s):
  1. Modeling and Simulation in Biomedical Engineering, Applications in Cardiorespiratory Physiology, Willem Van Meurs, McGrawHill, 2011
  2. Cardiac Electrophysiology Methods and Models, Daniel C. Sigg, Paul A. Laizzo, Yong-Fu Xiao and Bin He (Editors), Springer, 2010
Learning Objectives (Indicators)  

At the end of this course, the successful student will be able to:

  1. Apply principles from control systems (e.g. block diagrams, feedback loops), Electrical Engineering (e.g. LCR circuits), and Physics/Kinematics in combination with ordinary and partial differential equations to model physiological systems and processes. (1d)
  2. Apply and evaluate the suitability of various signal processing techniques to different types of physiological measurements (e.g. action potentials, ECG, EMG) for analysing signal characteristics and improving signal quality using Matlab. (2b), (3b), (5a)
  3. Apply numerical and analytical methods to generate computational models of physiological systems and simulate physiological signals (using Simulink and Matlab) to address biomedical problems (e.g. effect of pathologies or drugs on a system). (4b)
  4. Learn to identify and evaluate the implications of different approaches to addressing/modelling a biomedical problem and develop decision making criteria to determine the optimal solution under different conditions. (8b)
  5. Understand the underlying physiological, electrical, mechanical and chemical processes of human cells, tissues and organ systems that result in physiological signal generation and their role in generating biophysical models. (12b)

NOTE:Numbers in parentheses refer to the graduate attributes required by the Canadian Engineering Accreditation Board (CEAB).

Course Organization

3.0 hours of lecture per week for 13 weeks
1.0 hours of lab per week for 12 weeks
1.0 hours of tutorial per week for 12 weeks

Teaching AssistantsTBA
Course Evaluation
Theory
Midterm Exam 25 %
Quizzes (2*7.5%) 15 %
Final Exam 30 %
Laboratory
Lab (4 x 5%) 20 %
In-Class Assignments and Participation 10 %
TOTAL:100 %

Note: In order for a student to pass a course, a minimum overall course mark of 50% must be obtained. In addition, for courses that have both "Theory and Laboratory" components, the student must pass the Laboratory and Theory portions separately by achieving a minimum of 50% in the combined Laboratory components and 50% in the combined Theory components. Please refer to the "Course Evaluation" section above for details on the Theory and Laboratory components (if applicable).


ExaminationsMidterm Exam: The midterm exam will be in week 9 of the course (on March 11th). It will be a 2-hour, closed book test that will cover material from weeks 1-8.
 
 Quizzes: In week 7 (week of Feb. 26th) and week 11 (week of March 25th) of the course, will be of 30 minute duration at the start of tutorials 2 and 3, respectively. Quizzes are closed book and will cover lecture material from the previous 2-4 weeks.
 
 The final exam will be during the exam period, and will be 3 hours, closed book, and will cover all course material.
Other Evaluation InformationLaboratory manuals will be posted on the course shell on D2L. The lab will run every week beginning week 2. All labs will involve simulating and/or processing physiological signals and systems using Matlab and/or Simulink software.
 
 Each lab is worth 5%, and will be marked based on completion of the lab report and answering TA questions during and at the end of the lab session. A lab report must be submitted for each of the four labs, one lab report per group, submitted within 1 week of completing the lab (emailed to the TA before the start of the next lab). Late submissions will be penalized over the first 3 days, after which a grade of zero will be assigned.
 
 Lab reports will Not be accepted from students who did not attend a lab session.
 
 Lectures will involve in-class assignments that are to be submitted through D2L.
 
 ** Laboratory attendance and lecture attendance are both mandatory. Attendance will be taken within the first 15min of the lecture / lab start time. Late admission will not count towards one's attendance grade.
 
 The TAs are responsible for managing all quizzes and labs; kindly direct any related inquiries to them.
Other InformationLecture Time: Mondays 9AM -12PM, Location: DCC 350
 

Course Content

Week

Hours

Chapters /
Section

Topic, description

1

3

part I: 1

Lecture topics: Introduction to systems and modeling and physiological signals and
 noise. Review of signals and systems basics statistical description of a random process, continuous and discrete signals and digitization.


2

3

part I: 4

Lecture topics: Review of frequency decomposition of signals. Fourier series, Fourier Transform (discrete-time discrete fast short-time), wavelet transform, Laplace transform, filtering


3

3

part I: 1-2

Lecture topics: Differential equations and numerical methods, Modeling of the cardio-respiratory system


4

3

part I: 5, part II:1

Lecture topics: Modelling nerve action potentials, Stimulation of excitable tissue, Windkessel model


5

3

part I: 3,8, part II:3

Lecture topics: Feedback systems, control systems, system stability, sensory receptors
 


6

3

part II: 8

Lecture topics: Model validation, FEM, Immune System


7

3

part II: 7

Lecture topics: Linear model of blood flow, mechanical and electrical analogies


8

1

Lecture topics: Review for midterm exam (material from weeks 1-6)


8

2

(supplement)

Lecture topics: Modelling healthy and diseased ocular system


9

3

Midterm exam (in class, closed book)
 + 1hr to review solutions in the lecture


10

3

(supplemental lecture notes)

Lecture topics: Computational modelling of placental vasculature
 


11

3

part II: 4

Lecture topics: Modelling skeletal muscle contraction


12

3

part II: 4-5

Lecture topics: Modelling skeletal muscle contraction, Myoelectric activity


13

3

part II: 5-6

Lecture topics: EMG data acquisition and processing


14

3

(supplement)

Practice modelling a variety of physiological systems: Cellular iron regulation, fructose intolerance (through an exam mock-up)


Laboratory(L)/Tutorials(T)/Activity(A) Schedule

Week

L/T/A

Description

2-3

1

Lab 1: Wavelet transformation applied to EEG

4

T1

Tutorial 1: Introduction to Simulink

5,6

3

Lab 2: Windkessel model of blood circulation

7

T2

Tutorial 2: Review of course concepts problem solving

8-9

T1

Lab 3: System Identification

10-11

4

Lab 4: Immune System

12

T3

Tutorial 3: Skeletal Muscles

13

T4

Tutorial 4: Real-time data acquisition and signal processing

University Policies & Important Information

Students are reminded that they are required to adhere to all relevant university policies found in their online course shell in D2L and/or on the Senate website

Refer to the Departmental FAQ page for furhter information on common questions.

Important Resources Available at Toronto Metropolitan University

Accessibility

Academic Accommodation Support

Academic Accommodation Support (AAS) is the university's disability services office. AAS works directly with incoming and returning students looking for help with their academic accommodations. AAS works with any student who requires academic accommodation regardless of program or course load.

Academic Accommodations (for students with disabilities) and Academic Consideration (for students faced with extenuating circumstances that can include short-term health issues) are governed by two different university policies. Learn more about Academic Accommodations versus Academic Consideration and how to access each.

Wellbeing Support

At Toronto Metropolitan University, we recognize that things can come up throughout the term that may interfere with a student’s ability to succeed in their coursework. These circumstances are outside of one’s control and can have a serious impact on physical and mental well-being. Seeking help can be a challenge, especially in those times of crisis.

If you are experiencing a mental health crisis, please call 911 and go to the nearest hospital emergency room. You can also access these outside resources at anytime:

If non-crisis support is needed, you can access these campus resources:

We encourage all Toronto Metropolitan University community members to access available resources to ensure support is reachable. You can find more resources available through the Toronto Metropolitan University Mental Health and Wellbeing website.