Networks in the Brain and Biology
APSC 452/652, Spring 2006
Classroom: McGlothlin-Street Hall #20
Meeting times: M, T, F 11:00 - 11:50 AM

Instructor
Christopher A. Del Negro, Ph.D.
Office: McGlothlin-Street Hall #303
Lab: McGlothlin-Street Hall #318
Phone: 757-221-7808
e-mail: cadeln@wm.edu

Course Description
This course is a survey of networks in the brain and related physiological systems. Topics include mechanisms of cell-to-cell communication, classic brain circuits and their functional analyses, and collective emergent properties in natural systems, analyzed using graph theory and modeling approaches. Applications include simple neuronal networks in mammals and invertebrates, the heart, the pancreas, biochemical and genetic networks, collective behaviors of animals, and other forms of networks occuring in the natural world.

The course is roughly divided into three parts. The first part deals with neural circuits and cell-to-cell communication, our text here is Shepherd's Synaptic organization. The second part undertakes a general study of networks particularly applied to neurobiological and physiological systems; the principal text here is Barabasi's Linked. Part three deals with self-organized or decentralized systems in the natural world; we will draw principally from Camazine et al's Self-organization in biological systems.

This course is intended for advanced undergraduate and graduate students interested in biology, physics and applied mathematical research in neuroscience, cell and population biology, and biochemistry. There will be an open-book mid-term exam, as well as a paper due after the mid-term where you will be expected to analyze a brain or spinal network system using sources from the primary literature. Your final project will be to develop and simulate a self-organized/decentralized system using StarLogo or XPPAUT modeling software. You will present your modeling project to the class and prepare a written report for me. This final project will substitute for an in-class final exam.

Expectations
Class attendance is expected, but will not be monitored. Reading material includes textbooks and primary research literature, which is technically challenging. I will be available by telephone, email, or office visits to assist you in understanding the class material. This class will involve computer modeling using the following software: XPP-AUT and StarLogo. Homework will be collected and scored based on effort and participation, students should strive to get full credit on all homework assignments in order to augment their final grade. Keys to assignments will be posted to the course website. The College Honor Code must be upheld in all class-related activities; violations and violators will not be tolerated.

Grading
There will be one open-book mid-term exam (30%), one written assignment (30%), and a final project that has a class presentation and a written component (40%). The final project will be to develop a model of a network system, using StarLogo, and analyze its emergent or self-organized features. You should start the final project early in the semester to achive an insightful model and analysis. Final letter grades will be assigned according to the scale below: