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 
Web Site  http://terpconnect.umd.edu/~jzsimon/hlsc374/ or http://terpconnect.umd.edu/~jzsimon/bsci474/ 
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 nonlinear difference equations, eigenvector analysis, multidimensional 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 
Instructor  Jonathan Z. Simon, Professor  



Teaching Assistant  Shannon Kirby 

Day  Time  Location  

Simon  Tuesday  2:30  4:00 PM  AVW 2145 
Kirby  TBA  TBA  TBA 
Introduction & Basics Why Mathematical Modeling in Biology? Math Review Modeling Biological Populations Difference Equations Linear Biological Population Dynamics Nonlinear Biological Population Dynamics Equilibrium & Stability Matrix Algebra Linear StructuredPopulation Dynamics Eigenvector Analysis Nonlinear StructuredPopulation (e.g. PredatorPrey) Dynamics Phase Plane Analysis Multivariable Equilibrium & Stability Epidemiological Models Infectious Disease Models Nonlinear 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
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.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.
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.
Late Policy: 1 day late = 25% off, 2 days late = 50% off.
There is a weekly lab to test out newly learned modeling concepts on your computer. Lab reports should be turned in by uploading them electronically on ELMS. The labs are graded Pass/Fail: 100% for a strong report, 50% for a weak report.
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).
Due to credithours limitations, this course cannot have a separate Discussion section, so Office Hours become a critical resource. Professor Simon and the TA each hold separate office hours at nonoverlapping 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.
Each student is required to attend at least two “academic enrichment” seminars. This requirement can be satisfied by attending attending any scientific research seminar in the life sciences occurring outside of the normal class period, or in 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.
 1^{st} Exam: Tuesday, October 13 (subject to change)
 2^{nd} Exam: Tuesday, December 1 (subject to change)
 Final Exam: Tuesday, December 15, 8:00 – 10:00 AM
There will be no makeup exams. See Grading next for missed exam policies.
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 reweighted, if you give notice to the professor within 24 hours of the missed exam:
30% 1st or 2nd exam 40% Final exam
Discussing homework problems, and other ideas, with others is encouraged,
but,
your final writeup 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.
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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, 3013147613, or http://www.counseling.umd.edu/LAS. The educational counselors can help with time management, reading, math learning skills, notetaking and exam preparation skills. All their services are free to UMD students.