RYERSON UNIVERSITY

Course Outline (W2020)

BME809: Biomedical Systems Modelling

Instructor(s)Dafna Sussman [Coordinator]
Office: ENG317
Phone: (416) 979-5000 x 3767
Email: dafna.sussman@ryerson.ca
Office Hours: Fridays 9:30-10:30am (limited to 10min per student, 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 BME 229 and BME 639 and BLG 701
Antirequisites

None

Corerequisites

None

Compulsory Text(s):
  1. Signals and Systems in Biomedical Engineering: Signal Processing and Physiological Systems Modeling Second Edition, Suresh R. Devasahayam,. Academic/Plenum Publishers, 2012
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 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). (1b)
  2. 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. (1c), (12b)
  3. 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)
  4. 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)
  5. 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)

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
2.0 hours of lab/tutorial per week for 12 weeks

Teaching AssistantsMohamad‐Ali Bahsoun: mbahsoun@ryerson.ca
Course Evaluation
Theory
Midterm Exam 25 %
Quizzes (2 x 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 with "Theory and Laboratory" components, in addition to earning a minimum overall course mark of 50%, 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 for details on the Theory and Laboratory components.


ExaminationsMidterm exam in week 9 of the course (week of March 2nd) will be 1 hour, closed book and will cover material from weeks 1-7.
 
 Quizzes in week 6 (week of Feb 10th) and week 12 (week of March 23rd) of the course will be 15 minutes at the end of the tutorial session, closed book, and will cover material from the previous weeks.
 
 Final exam will be during exam period, and will be 3 hours, closed book, and will cover all material from weeks 1-13.
Other Evaluation InformationLab will run every week beginning week 2. Laboratory manuals will be posed on the course shell on D2L. 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 (to the TA at the start of the next lab).
 
 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 **
Other InformationNone

Course Content

Week

Hours

Chapters /
Section

Topic, description

1

3

2, 3

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


2

3

6

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

7

Lecture topics: Differential equations and numerical methods, State space models, Modelling of the cardio-respiratory system
 


4

3

8

Lecture topics: Modelling nerve action potentials
 Tutorial 1: Introduction to Simulink


5

3

4, 6

Lecture topics: Feedback systems, control systems, system stability, time-frequency domain analysis


6

3

14

Lecture topics: Model validation, Finite element analysis, immune system
 Quiz 1: on material from week 1-5


7

3

No lecture - Reading week


8

3

15

Lecture topics: Linear model of blood flow
 


9

1

Midterm exam (1 hour in class closed book) on material from weeks 1-6


9

2

10

Lecture topics: Skeletal muscle contraction


10

3

10, 11

Lecture topics: Modelling skeletal muscle contraction


11

3

7

Lecture topics: Electromyogram


12

3

7

Lecture topics: Numerical methods and geometry for graphics, Real-time data acquisition and signal processing
 Quiz 2: on material from week 9-11


13

3

Practice and review for final exam


Laboratory/Tutorials/Activity Schedule

Week

Lab

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

Policies & Important Information:

  1. Students are required to obtain and maintain a Ryerson e-mail account for timely communications between the instructor and the students;
  2. Any changes in the course outline, test dates, marking or evaluation will be discussed in class prior to being implemented;
  3. Assignments, projects, reports and other deadline-bound course assessment components handed in past the due date will receive a mark of ZERO, unless otherwise stated. Marking information will be made available at the time when such course assessment components are announced.
  4. Refer to our Departmental FAQ page for information on common questions and issues at the following link: https://www.ee.ryerson.ca/guides/Student.Academic.FAQ.html.

Missed Classes and/or Evaluations

When possible, students are required to inform their instructors of any situation which arises during the semester which may have an adverse effect upon their academic performance, and must request any consideration and accommodation according to the relevant policies as far in advance as possible. Failure to do so may jeopardize any academic appeals.

  1. Health certificates - If a student misses the deadline for submitting an assignment, or the date of an exam or other evaluation component for health reasons, they should notify their instructor as soon as possible, and submit a Ryerson Student Health Certificate AND an Academic Consideration Request form within 3 working days of the missed date. Both documents are available at https://www.ryerson.ca/senate/forms/medical.pdf.. If you are a full-time or part-time degree student, then you submit your forms to your own program department or school;
  2. Religious, Aboriginal and Spiritual observance - If a student needs accommodation because of religious, Aboriginal or spiritual observance, they must submit a Request for Accommodation of Student Religious, Aboriginal and Spiritual Observance AND an Academic Consideration Request form within the first 2 weeks of the class or, for a final examination, within 2 weeks of the posting of the examination schedule. If the requested absence occurs within the first 2 weeks of classes, or the dates are not known well in advance as they are linked to other conditions, these forms should be submitted with as much lead time as possible in advance of the absence. Both documents are available at www.ryerson.ca/senate/forms/relobservforminstr.pdf. If you are a full-time or part-time degree student, then you submit the forms to your own program department or school;
  3. Academic Accommodation Support - Before the first graded work is due, students registered with the Academic Accommodation Support office (AAS - www.ryerson.ca/studentlearningsupport/academic-accommodation-support) should provide their instructors with an Academic Accommodation letter that describes their academic accommodation plan.

Academic Integrity

Ryerson's Policy 60 (the Academic Integrity policy) applies to all students at the University. Forms of academic misconduct include plagiarism, cheating, supplying false information to the University, and other acts. The most common form of academic misconduct is plagiarism - a serious academic offence, with potentially severe penalties and other consequences. It is expected, therefore, that all examinations and work submitted for evaluation and course credit will be the product of each student's individual effort (or an authorized group of students). Submitting the same work for credit to more than one course, without instructor approval, can also be considered a form of plagiarism.

Suspicions of academic misconduct may be referred to the Academic Integrity Office (AIO). Students who are found to have committed academic misconduct will have a Disciplinary Notation (DN) placed on their academic record (not on their transcript) and will normally be assigned one or more of the following penalties:

  1. A grade reduction for the work, ranging up to an including a zero on the work (minimum penalty for graduate work is a zero on the work);
  2. A grade reduction in the course greater than a zero on the work. (Note that this penalty can only be applied to course components worth 10% or less, and any additional penalty cannot exceed 10% of the final course grade. Students must be given prior notice that such a penalty will be assigned (e.g. in the course outline or on the assignment handout);
  3. An F in the course;
  4. More serious penalties up to and including expulsion from the University.

The unauthorized use of intellectual property of others, including your professor, for distribution, sale, or profit is expressly prohibited, in accordance with Policy 60 (Sections 2.8 and 2.10). Intellectual property includes, but is not limited to:

  1. Slides
  2. Lecture notes
  3. Presentation materials used in and outside of class
  4. Lab manuals
  5. Course packs
  6. Exams

For more detailed information on these issues, please refer to the Academic Integrity policy(https://www.ryerson.ca/senate/policies/pol60.pdf) and to the Academic Integrity Office website (https://www.ryerson.ca/academicintegrity/).

Important Resources Available at Ryerson

  1. The Library (https://library.ryerson.ca/) provides research workshops and individual assistance. Inquire at the Reference Desk on the second floor of the library, or go to library.ryerson.ca/guides/workshops
  2. Student Learning Support(https://www.ryerson.ca/studentlearningsupport) offers group-based and individual help with writing, math, study skills and transition support, and other issues.