Time Schedule:
Wendy Thomas
BIOEN 485
Seattle Campus
Introduction to computational, mathematical and statistical approaches to the analysis of biological systems, including systems and control theory, molecular models and bioinformatics. Lectures and laboratory sessions emphasize practical problems in kinetics, metabolism and genomics. Prerequisite: CSE 143; BIOEN 305; MATH 308. Offered: A.
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 biology have allowed the formulation of increasingly sophisticated and realistic mathematical models of biological systems. This course is intended for students with a background in fields in biology or bioengineering seeking to learn to apply quantitative tools to biological problems.
Computational Topics Covered
Model Building Linear Systems Control Systems Transfer Functions Nonlinear Systems State Space and Stability analysis Parameter Estimation and System Identification Continuous Stochastic Systems Discrete Stochastic Systems Approximate Methods from Computational Biology
Student learning goals
Be able to recast a range of biological problems into quantitative models
Be able to choose appropriate computational tools
Be able to apply computational tools to solve a variety of biological problems.
Evaluate and articulate what value is added by a computational model
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 cell biology, metabolism, genomic analysis, protein structure, pharmacokinetics and regulatory networks are presented and will be used to motivate the lectures and closely integrate them with the laboratories.
Recommended preparation
Prerequisites are:
CSE 143: Computer Programming II or strong familiarity with a scientific programming language such as MATLAB. BIOEN 305: Introduction to the Bioengineering Analysis of Physiology II, or other physiology or cell biology. MATH 308: Matrix Algebra with Applications Background in ordinary differential equations is strongly recommended.
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.
Assignments will be graded on ability to perform simulations and analysis, and to evaluate how computational tools add to the understanding of the problem. 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 50% midterm projects 40% (20% each) class participation 10%
