HLSC 374 / BSCI 474: Mathematical Modeling in Biology

Section 0101
Fall 2015

Course Information

Lectures	Tu & Th 9:30 - 10:45 AM, CCC 1111
Lab	M 1:00 - 3:50 PM, CCC 1111 (starting 8/31/15)
Required Text	Elizabeth S. Allman, John A. Rhodes, Mathematical Models in Biology: An Introduction, Cambridge University Press, 2003, ISBN 9780521525862.
Recommended Text	David Quammen Spillover: Animal Infections and the Next Human Pandemic, W. W. Norton, 2013, ISBN 9780393346619.
Required Software	MATLAB: Mac Version or Windows Version (free for UMCP students)
Required Software	Microsoft Excel: Mac Version or Windows Version (free for UMCP students)
Prerequisites	Math 130 (Calculus for Life Sciences I), or the equivalent, including AP credits  Math 131 (Calculus for Life Sciences II), or the equivalent, including AP credits
Course Description	Students develop quantitative reasoning skills through the understanding of mathematically based biological models. Models are chosen from a variety of biological disciplines, including biological population dynamics, infectious disease propogation, molecular evolution, and phylogenetic trees. Mathematical skills developed include: solving non-linear difference equations, eigenvector analysis, multi-dimensional stability analysis, and the use of Excel and Matlab to implement these algorithms as computer models.
Testudo Info	http://www.sis.umd.edu/bin/seats?crs=HLSC374&sec=&term=201508 or http://www.sis.umd.edu/bin/seats?crs=BSCI474&sec=&term=201508

Other Course Pages

• Lab Supporting Files
• Reference Materials

Instructor Info

Office Hours

Outline (subject to change)

Introduction & Basics

Why Mathematical Modeling in Biology?

Math Review

Modeling Biological Populations

Difference Equations

Linear Biological Population Dynamics

Non-linear Biological Population Dynamics

Equilibrium & Stability

Matrix Algebra

Linear Structured-Population Dynamics

Eigenvector Analysis

Non-linear Structured-Population (e.g. Predator-Prey) Dynamics

Phase Plane Analysis

Multivariable Equilibrium & Stability

Epidemiological Models

Infectious Disease Models

Non-linear Infectious Disease Dynamics

Infectious Disease Phase Plane Analysis

Example: Sexually Transmitted Diseases

Mathematical Molecular Evolution

Probability

Modeling DNA Base Substitution

Markov Matrices

Phylogenetic Distances

Phylogenetic Trees

Computer Skills (simultaneously with rest of course)

Numerical Calculation & Modeling with MATLAB and Excel

Homework

Math is a “Learn it By Doing it” subject, making the homeworks critical.

 

Typically, homework problems will be assigned every week. It is possible that only some of the problems will be graded, but solutions will always be made available. Solution sets will be handed out as soon as reasonably possible after the homework is due. No credit will be given for any homework turned in after the solution set has been made available.

 

You must show your work—your method is more important than your result. For problems in which you use a calculator or computer, you must still explain your methods. A correct result without showing how you arrived at that result will not receive any credit.

 

All homework assignments are on ELMS, and all completed homework assignments should be turned in (not uploaded), at the beginning of class on their due date, typically on Thursdays.

 

Late Policy: 1 day late = 25% off, 2 days late = 50% off.

Labs

There is a weekly lab for you to try out newly-learned modeling concepts on your computer. Lab reports should be turned in by uploading them electronically on ELMS at the end of each lab session. The labs are graded Pass/Fail: 100% for a strong report, 50% for a weak report.

Laptop Computers

It is required that you bring a computer to all class meetings (including lab), and that you have working versions of Matlab and Microsoft Excel on that computer. Both software packages are free for UMCP students (see Required Software above for links by which you can obtain the software packages). 

Office Hours: Resource and Requirement

Due to credit-hours limitations, this course cannot have a separate Discussion meeting, so Office Hours become a critical resource. Professor Simon and the TA each hold separate office hours at non-overlapping times. Please take advantage of them!

 

Additionally, attending the office hours of Professor Simon, at least once in the first half of the semester, is required, counting one percentage point of the final grade. If you cannot make the standard office hours above, please make an appointment with Professor Simon for a different time.

Enrichment Reflections

Each student is required to attend at least two “academic enrichment” seminars. This requirement can be satisfied by attending any scientific research seminar in the life sciences occurring outside of the normal class period, or at the ILS Faculty Mentor Seminar Series. Students are required to write a short paper (about half a page) summarizing each seminar attended.

Your reflection should include:

• The title of the lecture/seminar
• Who was speaking and where they were from
• Why it was of interest to you
• What you felt you gained from the lecture
• Anything else you found interesting or if it opened you up to new ideas or ways of thinking

The grade value of each paper will be the same as a short homework.

Your Enrichment Reflections should be uploaded on ELMS.

Exams

• 1^st Exam: Tuesday, October 13 (subject to change) Tuesday, October 20
• 2^nd Exam: Tuesday, December 1 (subject to change)
• Final Exam: Tuesday, December 15, 8:00 – 10:00 AM

There will be no make-up exams. See Grading next for missed exam policies.

Grading

30%	Homework, Labs, Office Hours, Enrichment Reflections, etc.
20%	1st exam
20%	2nd exam
30%	Final exam

In the case of a 1^st or 2^nd exam missed for a legitimate reason, the other exam and the final will be re-weighted, if you give notice to the professor within 24 hours of the missed exam:

30%	1st or 2nd exam
40%	Final exam

Academic Honesty

Discussing homework problems, and other ideas, with others is encouraged, 

but,

your final write-up must be your own work and cannot be a copy of anyone else's work.

The University of Maryland, College Park has a nationally recognized Code of Academic Integrity, administered by the Student Honor Council. This code sets standards for academic integrity at Maryland for all undergraduate and graduate students. As a student you are responsible for upholding these standards for this course. It is also important to be aware of the consequences of cheating, fabrication, facilitation, and plagiarism. For more information on the Code of Academic Integrity or the Student Honor Council, please visit http://shc.umd.edu/SHC/.

Academic dishonesty includes copying homework answers from another‘s work, from previously written solution sets, from any book, from the web, or any other related source. Instances of academic dishonesty will be referred to the Office of Judicial Programs.

CourseEvalUM 

Your participation in the evaluation of courses through CourseEvalUM is a responsibility you hold as a student member of our academic community. Your feedback is confidential and important to the improvement of teaching and learning at the University as well as to the tenure and promotion process. CourseEvalUM will be open for you to complete your evaluations for two weeks near the end of the semester. Please go directly to the website http://www.courseevalum.umd.edu to complete your evaluations. By completing all of your evaluations each semester, you will have the privilege of accessing online, at Testudo, the evaluation reports for the thousands of courses for which 70% or more students submitted their evaluations.

Learning Assistance Service

If you experience difficulty in keeping up with the academic demands of a course, you should know about the Learning Assistance Service, 2201 Shoemaker Building, 301-314-7613, or http://www.counseling.umd.edu/LAS. The educational counselors can help with time management, reading, math learning skills, note-taking and exam preparation skills. All their services are free to UMD students.