Course Title: Simulating Neurobiological Systems (SYDE 556/750 topic 8)

Instructor: Chris Eliasmith (, HH 331)

Room and Time: E5 6127, Mon & Thurs. 12:30p-1:50p (2:00p-2:50p Thurs for 750)

Texts: Eliasmith and Anderson (2003). Neural Engineering: Representation, Computation and Dynamics in Neurobiological Systems. MIT Press.


Course Description: This course examines a general framework for modeling computation by neurobiological systems with an emphasis on quantitative formulations. Particular emphasis will be placed on understanding computation, representation, and dynamics in such systems. Students will learn how the fundamentals of signal processing, control theory and statistical inference, can be applied to modeling sensory, motor, and cognitive systems.

Prerequisites: Knowing how to program using matrices in some language (e.g. Python, MATLAB) is highly recommended. Familiarity with calculus and linear algebra is required.

Discussion Forum: You can sign up on to talk about the assignments, etc.:


Jan 5Chpt 1Introduction
Jan 9, 12Chpt 2,4Neurons, Population Representation#1 posted
Jan 16, 19Chpt 4Temporal Representation
Jan 23, 26, 30Chpt 5,6Feedforward Transformations#1 due (23rd at midnight); #2 posted
Feb 2, 6, 9Chpt 6,8Dynamics
Feb 13, 16Chpt 7Analysis of Representations#2 due (18th at midnight); #3 posted
Feb 20, 23*Reading Week*
Feb 27, Mar 2ProvidedSymbols
Mar 6, 9Chpt 8Memory#3 due (6th at midnight)
Mar 13, 16ProvidedAction Selection#4 due (13th at midnight)
Mar 20, 23Chpt 9Learning
Mar 27Conclusion
Mar 30, Apr 3Project Presentations

Grading: The course requires four assignments (60%) and a final project (40%). Assignments are due electronically by Midnight of the due date. Late assignments lose 1 mark per day. Assignments are to be done individually (everyone writes their own code and answers questions themselves).

Learning Objectives: By the end of the course students should be able to:

  1. Demonstrate a basic understanding of neural processes, neural mechanisms, theories of neural communication and computation, and theories of neural dynamics.
  2. Converse at a fundamental level with neuroscientists, psychologists, and neural and cogitive modelers.
  3. Design and Analyze simple and complex neural circuits for performing small- and large-scale neural computations.
  4. Apply engineering methods in signal processing, optimization, and control theory, among others, to characterizing and building neural circuits.
  5. Identify problems and solutions that may exploit the advantages of neural computation in an engineering context.

Academic Integrity: In order to maintain a culture of academic integrity, members of the University of Waterloo are expected to promote honesty, trust, fairness, respect and responsibility.

Discipline: A student is expected to know what constitutes academic integrity, to avoid committing academic offences, and to take responsibility for his/her actions. A student who is unsure whether an action constitutes an offence, or who needs help in learning how to avoid offences (e.g., plagiarism, cheating) or about "rules" for group work/collaboration should seek guidance from the course professor, academic advisor, or the Undergraduate Associate Dean. When misconduct has been found to have occurred, disciplinary penalties will be imposed under Policy 71 - Student Discipline. For information on categories of offenses and types of penalties, students should refer to Policy 71 - Student Discipline

Grievance: A student who believes that a decision affecting some aspect of his/her university life has been unfair or unreasonable may have grounds for initiating a grievance. Read Policy 70 - Student Petitions and Grievances, Section 4

Appeals: A student may appeal the finding and/or penalty in a decision made under Policy 70 - Student Petitions and Grievances (other than regarding a petition) or Policy 71 - Student Discipline if a ground for an appeal can be established. Read Policy 72 - Student Appeals

Academic Integrity Office (UW):

Accommodation for Students with Disabilities: The Office for Persons with Disabilities (OPD), located in Needles Hall, Room 1132, collaborates with all academic departments to arrange appropriate accommodations for students with disabilities without compromising the academic integrity of the curriculum. If you require academic accommodations to lessen the impact of your disability, please register with the OPD at the beginning of each academic term.

Intellectual Property: Students should be aware that this course contains the intellectual property of their instructor, TA, and/or the University of Waterloo. Intellectual property includes items such as:

  • Lecture content, spoken and written (and any audio/video recording thereof);
  • Lecture handouts, presentations, and other materials prepared for the course (e.g., PowerPoint slides);
  • Questions or solution sets from various types of assessments (e.g., assignments, quizzes, tests, final exams); and
  • Work protected by copyright (e.g., any work authored by the instructor or TA or used by the instructor or TA with permission of the copyright owner).

Course materials and the intellectual property contained therein, are used to enhance a student’s educational experience. However, sharing this intellectual property without the intellectual property owner’s permission is a violation of intellectual property rights. For this reason, it is necessary to ask the instructor, TA and/or the University of Waterloo for permission before uploading and sharing the intellectual property of others online (e.g., to an online repository).

Permission from an instructor, TA or the University is also necessary before sharing the intellectual property of others from completed courses with students taking the same/similar courses in subsequent terms/years. In many cases, instructors might be happy to allow distribution of certain materials. However, doing so without expressed permission is considered a violation of intellectual property rights.

Please alert the instructor if you become aware of intellectual property belonging to others (past or present) circulating, either through the student body or online. The intellectual property rights owner deserves to know (and may have already given their consent).