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Instructor Class Description

Time Schedule:

Wendy Thomas
BIOEN 485
Seattle Campus

Computational Bioengineering

Introduction to computational and mathematical analysis of biological systems, including control, stochastic, and transport systems. Lectures and laboratory sessions emphasize biochemical systems, but also include electrical, mechanical, and fluidic systems. Prerequisite: BIOEN 335; either AMATH 351 or MATH 307. Offered: Sp.

Class description

See the course web site http://courses.washington.edu/bioen485/ for the most up-to-date information about the course

BIOEN485 is a 4 credit class with lectures and laboratories. This course will cover methodological and practical aspects of the application of system analysis and computational tools to the solution of outstanding biological and biomedical problems. The advances both in computational power and the understanding of biology have allowed the formulation of increasingly sophisticated and realistic mathematical models of biological systems. This course is intended for students with a Introduction to computational and mathematical analysis of biological systems, including control, stochastic and transport systems. Lectures and laboratory sessions emphasize biochemical systems, but also include electrical, mechanical and fluidic systems. Offered jointly with BIOEN 585. Prerequisites: MATH 307 or AMATH 351; AMATH 301; BIOL 200, BIOEN 335. Topics Covered:

Model Building Model Verification Model Validation Linear Differential Equations and Control Systems Nonlinear Differential Equation Systems Continuous and Discrete Stochastic Systems Partial Differential Equation and Transport Models Parameter Estimation and System Identification

Student learning goals

Design quantitative models that represent a range of bioengineering problems, including identifying assumptions that are appropriate for the problem to be solved.

Choose and apply computational tools to solve these models.

Choose and apply analytic tools to verify computational solutions, including steady state and nondimensional analysis.

Evaluate how to validate bioengineering models with experiments.

General method of instruction

The course has two lectures and one three hour computational lab.

Recommended preparation

Note: THE PREREQUISITES IN THE COURSE CATALOG ARE INCORRECT AS OF Feb 18, 2013, but will be fixed within a few months. The correct prereqs are as follows for spring 2013:

Prerequisites:

MATH 307 (other ODEs, like AMATH 351 will substitute) AMATH 301(other programming like CSE 142 will substitute) BIOL 200 (other molecular/cellular biology like CHEME 355, ME 411 or EE 423 or PHYS 429 will substitute) BIOEN 335 (other mass transport or PDEs like CHEME 330, AMATH 353, MATH 309 or 324 will substitute)

Recommended:

MATH 308 or AMATH 352 (linear algebra) STAT 390 or IND E 315 (probability and statistics) BIOL 220 (physiology) BIOEN 315 or BIOC 405 (biochemistry) BIOEN 336 or ME 373 (systems analysis)

Class assignments and grading

Weekly Assingments involve some pencil-and-paper calculations, but mostly involve solving problems numerically using the software MATLAB.

Current literature will be assigned along with small written assignments and an in-class discussion.

Two projects will involve solving computational models based on published work and analyzing the contribution of the model to the medical or biological knowledge base.

All assignments will be graded on a 0.0 to 4.0 scale, representing a fail to an A. Your final grade will be the weighted average of these according to the following formula:

weekly assingments 40% quizzes 20% final project 30% literature analaysis 10%


The information above is intended to be helpful in choosing courses. Because the instructor may further develop his/her plans for this course, its characteristics are subject to change without notice. In most cases, the official course syllabus will be distributed on the first day of class.
Additional Information
Last Update by Wendy Thomas
Date: 02/18/2013