The basics

• Instructor: Dr. Ben Bolker. Contact me by (preferred method) e-mail via Avenue; e-mailing bolker@mcmaster.ca or visiting 412 Hamilton Hall, or (if necessary) phone 905-525-9140 x23320. My office hours for this semester have yet to be determined; meetings during office hours are preferred but I can also meet at other times by appointment. For more information about me, see my web page.
• Teaching assistant: Xiaojun Zhu (zhux23@mcmaster.ca).
• Class times and location: lectures Monday and Thursday 12:30-13:20, Tuesday 13:30-14:20 ABB/270, lab 8:30-9:20  BSB 244. Lecture periods may be used interchangeably, for computer work, lectures, or demonstrations. You are responsible for all material presented in either venue. Most lab times will be optional, for questions/additional computer work time, although a few will be used for make-up classes (see the syllabus).
  
• Textbook: Mooney and Swift (1999), A Course in Mathematical Modeling, Mathematical Association of America (ISBN  088385712X) [Amazon]. Other readings from primary and secondary sources will be made available on the web or through Avenue.
• Prerequisites: calculus II (one of MATH 1AA3, 1LT3, 1NN3, 1XX3, ARTS&SCI 1D06, ISCI 1A24); and (co-requisite) linear algebra (credit or registration in one of MATH 1B03, 1D03, 1H03, 1HH3; or one of MATH 1ZC3, 1ZZ5. ).
• Computer software and hardware: we will use the open-source R language throughout the course. It will be available on the computers in the lab, but it will be most convenient if you can install R on your own computer. (Lab hours (see above) are reserved for students in this course and you have priority over students not registered in this course at that time. However, you should also be able to work there outside of this allocated time-slot unless the computer lab has been reserved for some other course.) 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.
• Assessment: there will be a mid-term exam in class and a (1-hour) cumulative final exam during the time scheduled by the registrar's office. Other assignments will include weekly problem sets, written 'discussion questions' based on primary readings, and a group project (short progress reports and an individual, written report due at the end of the semester). Final grades will be based on the following components:
  

  component	weight
  class participation	10%
  assignments	20%
  projects	35%
  midterm	15%
  final exam	20%

• Course objective: To learn to apply mathematical tools to solve open-ended, real-world problems, to understand the benefits and limitations of mathematical modeling, and to critically assess the predictions based on mathematical models, as well as to stimulate interest in studying more advanced mathematics topics (e.g. numerical analysis, differential equations, probability and statistics, and optimization.) You can find a more detailed description of the course content and goals here.

Course Content

• The course will involve creative and empirical model construction. Given real-world scenarios, students will learn to identify a problem, make appropriate assumptions, propose a model, test the assumptions, refine the model if necessary, fit the model to data if appropriate, analyze the underlying mathematical structure of the model in order to appraise any sensitivity of the conclusions to the assumptions and model construction.
• Students will learn model analysis. Given a model, they will learn to work backwards to uncover any implicit assumptions, assess critically how well the assumptions reflect the scenario at hand, and estimate the sensitivity of predictions to modifications of the assumptions.
• The course will focus on modeling of dynamical systems, with an emphasis on biological systems; deterministic discrete-time, stochastic discrete-time, and deterministic continuous-time (ordinary differential equation) models will be covered.
• The computer language R will be introduced. This package can be used for graphical displays of data, numerical solutions of different dynamical systems, and simulation modeling.

Legal stuff

Policies

1. 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.
2. Policy on missed work or lectures: You should be aware of the Policy For Absence from School Due to Illness or Compassionate Reasons. It is important to know your rights and your responsibilities. If you must miss a presentation or cannot submit assigned work on time for a valid reason (e.g., medical reasons, etc.) you may be able to obtain an excused absence by taking appropriate documentation (e.g. note from physician) to the Faculty/Program office and then discussing this with your instructor. If the Faculty/Program gives its approval, the final examination will then be given the appropriate extra weighting. Otherwise, a grade of zero will be entered for the missed work.
   
   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.
   
   
3. Policy on late work: All assignments are due in class on the specified date, or e-mailed prior to class, unless otherwise stated. I reserve the right to penalize late work by 10\% per day.
4. 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:

   A+	A	A-	B+	B	B-	C+	C	C-	D+	D	D-	F
   12	11	10	9	8	7	6	5	4	3	2	1	0
   90-100	85-89	80-84	77-79	73-76	70-72	67-69	63-66	60-62	57-59	53-56	50-52	0-49

   (from p. 29 of the current Undergraduate calendar)
   
   
5. No calculators or other aids will be allowed during examinations unless explicitly indicated.
   
   
6. You will be required to bring your official McMaster University photo identification card to the final examination.
   
   
7. Students' grades will be posted in Avenue 2 Learn.

Academic Integrity

You are expected to exhibit honesty and use ethical behaviour in all aspects of the learning process. Academic credentials you earn are rooted in principles of honesty and academic integrity.

Academic dishonesty is to knowingly act or fail to act in a way that results or could result in unearned academic credit or advantage. This behaviour can result in serious consequences, e.g. the grade of zero on an assignment, loss of credit with a notation on the transcript (notation reads: "Grade of F assigned for academic dishonesty"), and/or suspension or expulsion from the university.

It is your responsibility to understand what constitutes academic dishonesty. For information on the various types of academic dishonesty please refer to McMaster's academic integrity web page.

Here are four common examples of academic dishonesty:

1. Plagiarism: For example, the submission of work that is not one's own or for which other credit has been obtained.
2. Improper collaboration: In this course, you are encouraged to discuss the assigned problems with other students in your class. However, when the work is not explicitly assigned as a group project you must write the solutions in your own words without referring to any other students' work. The copying or even paraphrasing of anyone's solutions will be considered academic dishonesty. For group projects, you will be asked to report your own assessment of how you contributed to the group's work.
3. Copying or using unauthorized aids in examinations: In this course you are not allowed to talk to or communicate in any way (e.g. pass notes) with anyone but the instructor or the invigilators during an examination.
4. Continuing to write once the announcement that the alloted time for a test or examination is over without the express consent of the instructor or one of the invigilators.

This outline will be linked from the course home page. However, it is your responsibility to check the course home page and syllabus regularly for further announcements, course handouts, assigned work and their due dates, information about test dates and locations when this information becomes available, downloadable course related material, etc. Recorded marks for tests and assignments will be posted on Avenue. You should check these once they become available and bring any discrepancies to the attention of the instructor or TA as soon as possible.