March 21, 2018, Wednesday
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APPM 4390/5390

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Essential Mathematical Biology
Dynamic Models in Biology

Course: Mathematical Biology, Spring 2018
Professor: Danielle Lyles
Office: ECOT 343

Class website: APPM 4390/5390
Office Hours: MW 11-12 in ECOT 343 and W 4-5 in FLMG 208, OR BY APPOINTMENT

Essential Mathematical Biology
Corrections to early printing
By: Nicholas F. Britton
ISBN 1-85233-536-X
Dynamic Models in Biology
By: Ellner & Guckenheimer
ISBN 0-69112-589-9

Lectures: MWF 1-1:50PM, DUAN G1B35


The goal for this class is for students to develop a fundamental understanding of how mathematics is applied as a tool to aid in studying complex systems in the biological sciences. We will thoroughly investigate case studies in several fields including: Molecular Systems Biology, Sea Turtle Ecology, Glucose Metabolism, HIV Pathogenesis, and Microbial Community Dynamics. Graded work will include a mix of theoretical and computational homeworks and short research projects, culminating in a final group project.

Practically speaking, this class is designed for advanced undergraduate and beginning graduate students in the mathematical, physical, and biological sciences with a solid mathematical background, i.e., Linear Algebra and Differential Equations. The course prerequisite (which can be waived with instructor approval) is APPM 2360 (Differential Equations & Linear Algebra) & 3310 (Matrix Methods), and may be taken simultaneously with this course. Also note that familiarity with matlab or other programming language is assumed (prerequisites include classes which use matlab).

Course Grade:

About 8 Homeworks: 55%

3 Projects: 45%

The syllabus, projects, homework, and homework solutions will be posted in D2L.


Homeworks will be due roughly once every week to two weeks. For the computational aspects of the course, we will be using the SimBiology toolbox in Matlab. Now that CU has a site license, everyone should have access to this in ECCR 147.

• In general, late homework will not be accepted.


There will be three projects during the course of the semester. The first is designed to get you involved in contributing to the mathbio wiki and due roughly 1/3 of the way through the semester. For the second, you will get to work in groups and write a wiki page describing a classic model in mathematical biology and due 2/3 of the way through the semester. For the last project, you also get to work in groups (if you wish) and will have the option of choosing from a list of suggested topics or finding your own. Again, you will be required to create a wiki page. You/your group will also make a presentation sometime during the last two weeks of the semester. Stay tuned for more information.

Note that the distinction between 4390 and 5390 lies in the third project expectations. For 4390, students are expected to reproduce a result in the literature. For 5390, students are expected to develop their own model or extend an existing model of the biological phenomena of interest.

Lastly, the wiki will be at