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Instructor Class Description

Time Schedule:

James Bassingthwaighte
Seattle Campus

Special Topics

Topics of current interest in the field, offered as lectures, conferences, or laboratory. Offered: AWSpS.

Class description

Quantitative and integrative treatments of transport and metabolism of solutes and their reactions in physiological systems, as appropriate for the modeling of metabolism and drug therapy. Part I: Basic transport mechanisms: molecules in fluids, convection, diffusion, filtration, permeation, binding processes, solubility and partition, reactions, transmembrane transporters, enyzymes, channels, pumps and electrophysiology, integration at the cellular level. Part II: Mass transport in the circulatory system, convection-diffusion, heterogeneity of perfusion in organs, pressure-flow dynamics, networks, blood-tissue exchange processes tracer techniques, gas transport in blood, airway and alveolar exchange, in vivo imaging and metabolism, renal solute and water exchanges.

Student learning goals

Learning how to translate qualitative physiological descriptions into models of the system

Use quantitative approaches to understanding biological systems

Reconciling contradictions amongst data sets.

Composing and running model solutions to analyze and parameterize data

Testing concept and mathematical models against data

using optimization techniques and Monte carlo methods to define parameter confidence limits

General method of instruction

Use a textbook, partially written, as the basis for lecture-discussions

Recommended preparation

BIOEN 503, biochemistry, Ordinary and partial differential equations

Class assignments and grading

1. Solving problems, mostly those given in the text book. 2. Team Research Project: Develop a computational model of a physiological system on which there are data available, but for which there is not a model available on SBML, CellML or Physiome sites. The modeling should be taken to a level consistent with the teaching or research models up on the website, and of sufficient complexity and originality to merit recognition as useful. 3. Individual class contributions: presentation. discussion activity, questions illustrating desire to learn and to teach others 4. Writing skills in presenting modeling and physioloogical discourse.

Homework: Bi-Weekly question sets. 30% Class participation in discussion: 20% Team grade:(same for all) 30% Final Writeup: 20% of grade

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 James Bassingthwaighte
Date: 12/08/2013