Syllabus

Simulation of Biocomplexity
Biology Topics Seminar: Computer Simulation of Biological Systems
Fall Semester 2009


This course is cross-listed in the College of Science Biology Department (BIOS60579) and the College of Engineering Computer Science Department (CSE40539/CSE60539). The course will cover computer-modeling techniques for simulating the behavior of biological and public health systems. The primary approach will be the individual-based modeling method (sometimes called the agent-based approach). Special focus will be given to modeling various biological systems: for example, the epidemiology of malaria, population ecology, evolutionary dynamics, microbial ecology, genetic regulatory networks, animal behavior, developmental biology, etc. Topics include methods for modeling and simulation, statistical distributions, random variate generation, animation, visualization, design of simulation experiments, verification and validation of simulations, and analysis of results. Biological Sciences students will work on collaborative projects with computer science majors. Students will be expected to learn about 1) simulation and modeling, 2) to help define biological problems for modeling and simulation, and 3) to help with verification, validation and interpretation of results. (Computer programming on course projects will be done by the computer science students.) A major objective of the course will be to compare the performance of specific biological models when simulated through individual-based versus classical approaches.

Instructors:

Frank Collins (Biological Sciences), frank@nd.edu
Greg Madey (Computer Science & Engineering), gmadey@nd.edu

Office Hours:

Collins: Tuesday/Thursday, 10:45 - 11:45, and by appointment
Madey: Tuesday/Thursday, 10:45 - 11:45, and by appointment

Time/Location:

Tuesday/Thursday, 9:30A - 10:45A, DeBartolo Hall 140

Texts:

No formal textbook will be required. Online articles and research papers will compose the course readings.

Course Goals:

The goals of this course include: 1) the student will learn how (in collaboration with biological science students) to define, design, develop, implement and analyze computer simulations of biological systems, 2) learn about languages, libraries and tools for building simulations, and 3) how to design simulation experiments, verify and validate simulations, and to interpret results of computer simulation based experiments.

Prerequisites:

CSE40539/CSE60539: Undergraduate major in CSE or graduate student in CSE (required), and any course in statistics or probability (suggested but optional).

BIOS60579: Biology major (required), and any course in statistics or probability (suggested but optional).

Computer Usage:

Course content will be project driven. Multiple modeling and simulation projects will be assigned. At least one large project will be assigned requiring the preparation of research paper. Biology students will be expected to help specify and design models & simulations, execute the simulations, and to interpret and analyze simulation output.