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Course Description

Intended Audience

Goals of the course

Specific objectives

Course format

Grading Policy

General approach

 

 

MEDED 534 , Autumn 2005
Biology and Informatics

Course Overview

Course Description
An introduction/review of some of the fundamental concepts or fields in biology, the information representation and management problems that arise from these fields, and current and potential informatics solutions to these problems.

Intended Audience
Primarily students with technical backgrounds, in areas such as computer science, electrical engineering, information science and related fields. Students with a biology background may also find the course of benefit because of the emphasis on informatics.

Goals of the course

  • To introduce or review fundamental concepts in both classical and modern biology that will provide a basis for understanding specific biological research areas and the associated informatics.
  • To show how these concepts give rise to information representation and management problems that drive research in biomedical informatics.
  • To illustrate specific biomedical informatics research areas applicable to basic biomedical research.
  • To give the student sufficient understanding of both the biology and informatics that they can pursue biomedical informatics research.

Specific objectives

  • Understand the fundamental core concepts and vocabulary in classical and modern biology
  • Learn specific facts and knowledge for one or two examples related to these concepts
  • Learn how to find additional facts and knowledge for any given field
  • Know the primary information representation and management issues that arise from each of these fields
  • Know about example solutions to these problems, and where to find more solutions.
  • Create a personal conceptual framework for organizing the knowledge learned
  • Know what else one needs to learn in order to pursue informatics research or development in one of these fields.

Course format
One 1.3 hr lecture, one 1.3 hr lecture/discussion/computer lab each week.

Grading Policy
Grades will be based on one take-home midterm exam, a final project, two class presentations, and general class participation. Approximate weighting:

Midterm 30%
Class Presentations 20%
Final Project 30%
Class Participation 20%

General Approach
The subject material is primarily organized along the structural hierarchy, from macro (visible) to molecular. This hierarchy reflects the predominant structural approach to understanding in biology, and also reflects the historical accumulation of biological knowledge from the macro to the currently predominant molecular level.

The first part of the course is devoted to human biology at the macroscopic (organs), and microscopic (tissues and cells) levels, along with an overview of physiology (function) at the macroscopic level. These levels correspond to "classical" human biology, of the type that is traditionally taught in the first year of medical school, and that has existed in some form for several hundred years. The information associated with these levels is primarily descriptive in nature, as was biology itself for most of its existence. Nevertheless, an understanding of the basic organization and functioning of the body at these levels provides a useful framework for placing in context the causal mechanisms being uncovered at the molecular level. Much of current medical practice is concerned with the functioning of the body at these levels.

These classical fields are generally known, so there is little new biological research. However, they form the foundation for clinical medicine as well as a framework for relating the new work arising at the molecular level to clinical manifestations of disease. They are therefore a source of much new research in informatics.

The second part of the course is devoted to basic concepts of "modern" biology that have sprung up beginning in the mid-20th century, and which now form the bulk of the biological research endeavor. In this case the structural direction is reversed, starting from the atomic and molecular level, moving to macromolecules and cells. These topics start with basic biochemical concepts such as covalent bonds, kinematics, and metabolic pathways, followed by proteins and their multiple functional and structural roles. DNA and its role in protein synthesis is then followed by gene regulation (how protein synthesis is controlled in individual cells) and cell-cell signaling (how cells communicate with each other). An understanding of these topics is fundamental to understanding much of current biomedical research.

The next two topics consider the application of these basic biological principles to two biomedical research areas: developmental biology and neuroscience. Developmental biology seeks to understand how the complete organism develops from the fertilized egg, whereas neuroscience seeks to understand the functioning of the brain and nervous system. Both these areas are extremely active currently, and both generate prodigious amouts of data that lead to complex informatics research problems.

One week is devoted to each topic. The first (Monday) session is generally a lecture given by an expert biologist in the field. This lecture, which is augmented by assigned readings, introduces the basic concepts and vocabulary of the field. Many of the readings are chapters in the course textbook, "Molecular  Biology of the Cell", by Alberts.

For each topic the general concepts are often illustrated with more detailed information about a single structure or system, in order to make the concepts more concrete, and to give a flavor for the way these structures are studied in the full medical first year curriculum. The same structures will be used to illustrate the general concepts for each of the classical topics. In this quarter we will use the lung and occasionally the heart as examples. Therefore, by the end of the week 4 the students will know something about the gross and macroscopic anatomy of the lung, the structure of lung cells, and the physiology of respiration. The integration of such information for a single organ system (in this case the respiratory system) is usually studied in the organ systems courses in the second year of medical school, as a preparation for clinical medicine. Thus, an introduction to the notion of an organ system runs as a separate thread throughout the initial part of the course.

The second (Wednesday) session for a given topic is devoted to the informatics issues and research that arise within the given core concepts. At the end of the Monday lecture students are given the assignment of thinking about the data and knowledge associated with the given field, as well as the information representation and management issues that therefore arise. On Wed selected students will review publications and often working systems describing informatics research in these issues, and the class together will explore informatics solutions that have been developed to deal with them.

By the end of the course the students should be able to generalize the methods and knowledge learned from a given field or sub region of the body and apply these methods to most other regions.

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 Last Updated:
9/8/05

Contact the instructor at: brinkley@u.washington.edu