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Instructor Class Description

Time Schedule:

Paolo Vicini
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

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 recent, rapid development of these fields requires an understanding of the mathematical, statistical and computational tools behind such a rapid growth. The advances both in computational power and the understanding of [cell- and organ-level] biology have allowed the formulation of increasingly sophisticated and realistic mathematical models of biological systems. The course objective is to teach the students how to recast their biological knowledge as a quantitative model of the system.

Student learning goals

General method of instruction

The material of the course is balanced between theoretical and practical fundamentals and specific case studies, closely integrated with current literature reviews and computer laboratory sessions. Examples from biology, metabolism, genomic analysis, protein folding and pharmacokinetics are presented and will be used to motivate the lectures and closely integrate them with the laboratories.

Recommended preparation

Prerequisites include: CSE 143: Computer Programming II; BIOEN 305: Introduction to the Bioengineering Analysis of Physiology II; MATH 308: Matrix Algebra with Applications. Background in ordinary differential equations is strongly recommended. Equivalent coursework may be substituted for the prerequisites on an individual basis. Please consult the instructor if you are not sure you meet the prerequisites for taking this course.

Class assignments and grading

Grading is based on: lab reports 30%, homework 30%, midterms (two take-home projects) 30%, class participation 10%. Normally, laboratory reports are due in class one week after the lab, homework assignments are due one week after distribution by 5 p.m. Exact dates are specified on this website. No late reports will be accepted, so please turn in everything you were able to accomplish in the allocated time. There are two midterms for this class and no final exam will be administered. Class participation is measured from the weekly literature discussions based on the Article of the Week.


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.
Please follow this link for updated information
Last Update by Paolo Vicini
Date: 09/05/2003