PHYSIOL 520 (BIOI 520) - Computational Systems Biology in Physiology - 3 Credits

Term:Winter 2015

Days:Wednesday 9:00-10:00 AM (MS II 7745)
Fridays 1:00-3:00 PM (Palmer Commons 2036)

Course Director:Santiago Schnell

Faculty Instructors:Daniel Beard, Brian Carlson, Santiago Schnell, and Kalyan C. Vinnakota

Course Description This course provides an introduction to the modeling in systems biology for both experimental and theoretical inclined students, as well the currently employed strategies to investigate physiological problems with computational modeling. Our approach is innovative. Most modeling courses present collections of useful mathematical or computational techniques and illustrate the various techniques by solving classical problems. However, in our course, we select important physiological problems whose solution will involve some useful computational modeling.  After briefly discussing the required scientific background, we formulate a relevant computational problem with some care. The formulation step is often difficult.  Not many courses or textbooks actually demonstrate this. In our course, we plan to give due emphasis to the challenges involved in constructing computational models. This approach will empower student to build their own models, and become effective costumers of systems biology research. Background in mathematics or computing is not required.

Audience:This course is aimed graduate students in the Program in Biomedical Sciences. We also welcome interested advanced undergraduates, postdoctoral fellows and other research staff.

Prerequisites:An introductory course in calculus is desirable but not essential. No former programming experience is needed, but a working knowledge of using computers will make the learning curve much more pleasant.

MATH 564 - Topics in Mathematical Biology: Clocks, Rhythms and Oscillations

Term:Winter 2015

Days:Tuesday 11:30 AM-1:00 PM
Thursday 11:30 AM-1:00 PM

Faculty Instructor:Forger

Course Description From sleep-wake patterns, heartbeats, locomotion and firefly flashing to the treatment of cancer, diabetes and neurological disorders; oscillations are of great importance in biology and medicine. Mathematical modeling and analysis are needed to understand what causes these oscillations to emerge, properties of their period and amplitude and how they synchronize to signals from other oscillators or from the external world. The goal of this course will be to teach students how to take real biological data, convert it to a system of equations and simulate and/or analyze these equations. Models will typically use ordinary differential equations. Mathematical techniques introduced in this course include 1) the method of averaging 2) methods for fitting data 3) Fourier techniques 4) entrainment and coupling of oscillators 4) phase plane analysis and 5) various techniques from the theory of dynamical systems. Emphasis will be placed on primary sources (papers from the literature) particularly those in the biological sciences. Consideration will be given in the problem sets and course project to interdisciplinary student backgrounds. Teamwork will be encouraged.

Text:No textbook is required.

Prerequisites:Differential equations and linear algebra. Math 463 is an excellent preparation.