The basics

Course web page

http://www.math.mcmaster.ca/bolker/classes/m747/

Time and place

Mon/Th 9:30-11:00 HH (Hamilton Hall) 312

Prerequisites

ODEs, linear algebra, some experience with mathematical/numerical computation.

Instructor

Dr. Benjamin Bolker

• e-mail: bolker@mcmaster.ca.
• Office: HH 314
• phone (e-mail strongly preferred!) 905-525-9140 x23320)

Office hours

To be determined. Meetings during office hours are preferred but I can also meet at other times by appointment.

Calendar description

Development of mathematical models using differential equations, difference equations, stochastic processes and/or game theory. Analytical and numerical exploration of the models. Topics selected from ecology, epidemiology, immunology, physiology and/or other areas of biological and medical science.

Textbook

None.

Timetable

schedule.html

Computer use

we will use the open-source R language throughout the course. It will be most convenient if you can install R on your own computer. I hope that it will be possible for students to bring (or share) a laptop for work during class sessions. A backup device such as a memory stick is required in order to save your work.

Scope

The scope of the course will largely be determined at the organizational meeting. I have three ideas, listed in order of current support (representing only a small number of conversations):

• a broad survey of approaches to stochastic models in math biology, with an emphasis on non-rigorous but practical approximate and computational solutions;
• parameter estimation techniques for mathematical biology, with a particular focus on parameter estimation for stochastic dynamical systems;
• introduction to the theory of the evolution of virulence, resistance and tolerance in host-pathogen systems

Assignments and assessment

The course will consist of readings and discussion of models and techniques from the primary literature and a class project. Students will be responsible for

• reading assigned material prior to class and participating in an on-line forum discussion of the material (minimally, posting discussion questions prior to class) as well as in-class discussion (25% of grade);
• taking primary responsibility for presenting material, one to three times during the course of the semester (depending on class size and organization: 35% of grade);
• completing a class project (possibly in a groups, depending on class size), with a 5–10 page write-up due at the end of the semester (40% of grade).

Grading scheme

I reserve the right to change the weightings in the grading scheme. If changes are made, your grade will be calculated using the original weightings and the new weightings, and you will be given the higher of the two grades. At the end of the course the grades may be adjusted but this can only increase your grade and will be done uniformly. I will use the following grade chart to convert between letter grades, grade points and percentages:
__________________________________________________________________________________

(from p. 29 of the current Undergraduate calendar)

The course goals are to gain knowledge of and experience with a broad range of analytical and computational techniques in mathematical biology; to practice and improve ability to read, critique, and replicate results from the primary mathematical biology literature and to formulate and analyze novel models that are both biologically and mathematically sensible.

Legal BS

Dates subject to change

The instructor and university reserve the right to modify elements of the course during the term. The university may change the dates and deadlines for any or all courses in extreme circumstances. If either type of modification becomes necessary, reasonable notice and communication with the students will be given with explanation and the opportunity to comment on changes. It is the responsibility of the student to check their McMaster email and course websites weekly during the term and to note any changes.

Absences and missed work

If you are absent from the university for a minor medical reason, lasting fewer than 5 days, you may report your absence, once per term, without documentation, using the McMaster Student Absence Form. Absences for a longer duration or for other reasons must be reported to your Faculty/Program office, with documentation, and relief from term work may not necessarily be granted. When using the MSAF, report your absence to course_email@mcmaster.ca. You must then contact the instructor immediately (normally within 2 working days) by email (see above for contact information) to learn what relief may be granted for the work you have missed, and relevant details such as revised deadlines, or time and location of a make-up exam. Please note that the MSAF may not be used for term work worth 30% or more, nor can it be used for the final examination.

If you must miss a lecture, it is your responsibility to find out what was covered. The best way to do this is to borrow a classmate’s notes, read them over, and then ask your instructor if there is something that you do not understand.

Late work

All assignments are due in class on the specified date, or e-mailed or posted to Avenue 2 Learn prior to class, unless otherwise stated. I reserve the right to penalize late work by 10% per day.

Academic honesty etc.

The expectations for this class are fairly simple: however, if you have any questions please ask. See the McMaster Office of Academic Integrity’s web page for general information.

• You may work collaboratively on class projects where indicated, but you must follow my instructions about separate write-ups or indicating division of labor.
• It’s unlikely to come up in this course, but you should be aware of the definition of plagiarism; be sure to appropriately cite any sources that you use.
• When in doubt about any other ethical issues that arise from the class, please don’t hesitate to contact the instructor.