MTH 427/527: Introduction to Mathematical Biology
Fall 2017

from www.jdirving.com and from www.thesystemsthinker.com

Professor

Dr. Vrushali Bokil
Office: Kidder 048
Office Hours: M 1-2pm, W noon-1pm, F 2-3pm or by Appt.
Email:Click to email: bokilv at math dot oregonstate dot edu
Note: Outside of class and office hours, questions should be addressed via email. Emails will be answered during working hours between 9am-5pm. Depending on my schedule, emails may not get answered the same day. So please allow 24 hours for a response.

Class Grader

Charles Camacho
Office: Kidder 314
Office Hours: Wed 9-11 am (in Kidder 314)
Wed 1-2 pm and 3-5 pm (in the MLC)
Email:Click to email: camachoc at math dot oregonstate dot edu
Note: For questions related to homework and lab assignments, you may contact Charles. However, for questions on class material please contact Dr. Bokil


Course Information

Time/Classroom: MWF 11:00-11:50 am, STAG 260

Registration Details: CRN: 24166, Section: 001

Prerequisites: (MTH 256 or MTH 256H) and MTH 341. All courses used to satisfy MTH prerequisites must be completed with a C- or better.

Required Textbook :
Mathematical Models in Population Biology and Epidemiology:
Series: Texts in Applied Mathematics, Vol. 40.
Authors: Fred Brauer and Carlos Castillo-Chavez [BC]
2012.

Course Description:
Mathematical modeling, analysis and simulation play a key role in biology and epidemiology. In this introductory course, modeling and mathematical analysis of biological processes using first principles will be introduced. The course will consider deterministic models in continuous time for population models and models for the spread of pathogens in a variety of settings. The models will be analyzed using linearization principles, linear and nonlinear stability techniques, phase plane methods. As time permits we will also consider structured models, discrete time models, and spatial models with diffusion (metapopulation and PDE based models). Results obtained from mathematical analysis will be qualitatively interpreted and applied to the biological process under investigation. We will also discuss fitting of models to data and illustrate the numerical solution of models and data fitting using MATLAB code.

Learning Outcomes: Students completing Math 427/527 will be able to:

  • Obtain an intuitive and working understanding of some well-known mathematical models for population dynamics and epidemiology and their mathematical analysis.
  • Be able to analyze models based on differential equations using linearization principles, linear and nonlinear stability techniques, phase plane methods.
  • Qualitatively interpret results obtained from mathematical analysis of models, and apply to the biological process under investigation.
  • Develop some experience in the implementation of numerical methods by using a computer. More specifically, utilize MATLAB codes to simulate simple discrete and continuous time models.

Reading Assignments: Look at the Calendar for sections that will be covered in class for each lecture. Reading material will be assigned in class. NOTE: While it may not be stated explicitly each day, students are expected to read each section to be covered before class. Questions not addressed during class time should be asked in office hours. Students are responsible for any material missed due to absence.

MATLAB We will work on some simple programming in MATLAB to simulate differential and discrete equations. If you have not used this language before you will have time to understand the basics of MATLAB during the first week of classes. A number of different introductory tutorials are available on my website. The textbook presents an introduction to MATLAB in Appendix D; and the programs in the text serve as further examples. Students are encouraged to modify these programs and to use them as models for writing their own MATLAB programs. Look at MATLAB resources for more help.


Course Grading

  • Written Assignments (20%): There will be approximately four-five written assignments this term. Due dates/times will be posted on the Course Calendar. Late assignments will not be accepted and will not receive any credit. Written assignments will be based on problems from the text. Students must complete assignments individually.
    Assignments will be posted on Canvas:

  • Computational Assignments (20%): There will be approximately four-five computational assignments this term, which will comprise writing code in MATLAB. Due dates/times will be posted on the Course Calendar. Late assignments will not be accepted and will not receive any credit. Students must complete computational assignments individually. A HARDCOPY of the relevant output must be turned in along with detailed explanations of solutions and supporting plots. PLEASE DO NOT EMAIL YOUR CODE either to me or the grader for this course.
    Computational assignments will be posted on Canvas:

  • Midterm (25%): Tentatively scheduled for Friday, October 27th, 2017, in STAG 260 at 11:00 am. There will be no makeup exams. Absence from the midterm gives a score of 0 for the midterm. Books, notes, or graphing/programmable calculators will NOT be allowed on exams. Exam problems will be based on class lectures and assigned homework problems.

  • Final (35%): A comprehensive final exam will be given on Thursday, December 7th, 2017 from 9:30-11:20 am in BEXL 103 (Room subject to change. Please look at this webage for updates). This date and time is set by OSU. Scheduling conflicts with the final exam must be resolved in advance. The Final Exam will be comprehensive, counts the equivalent of two midterm exams, and will serve as a make up for the midterm. Books, notes, or graphing/programmable calculators will NOT be allowed on the final exam.

Course Grade Scale: The Grade for the course is determined by the best two of three exam scores and the written and computational homework assignments. Each letter grade below corresponds to grades scored between the lower limit (including) and less than the upper limit (excluding).
A 90 - 100%
A- 87 - 90%
B+ 84 - 87%
B 80 - 84%
B- 77 - 80%
C+ 74 - 77%
C 70 - 74%
C- 67 - 70%
D+ 64 - 67%
D 60 - 64%
D- 57 - 60%
F below 57%


Class Details and Announcements: Students should check this class website and the Canvas classpage for general information, announcements, assignments, due dates, exam dates and other policies regarding the class.

Special Arrangements and Course Drop/Add Information

  • Disability Access: Accommodations for students with disabilities are determined and approved by Disability Access Services (DAS). If you, as a student, believe you are eligible for accommodations but have not obtained approval please contact DAS immediately at 541-737-4098 or at Disability Access Services. DAS notifies students and faculty members of approved academic accommodations and coordinates implementation of those accommodations. While not required, students and faculty members are encouraged to discuss details of the implementation of individual accommodations.
  • Makeup Policy: For make-up exams for official or emergency reasons and other special arrangements, please read the University's official policy Student Petitions to Change the Time of an Exam Please contact Professor Bokil to make arrangements. For all types of special arrangements appropriate documentation will be required.
  • Course Drop/Add Information: See Office of the Registrar and Academic Calendars



My Links:

Canvas
Class Calendar
MATLAB Resources


Other Links: