HONORS 396C: Autumn 2010 course information

Check here for homework assignments, course notes, and other hopefully useful stuff.

Tentative lecture schedule

The topics we will cover are tentatively scheduled, though we may slip or add or substitute other topics.

Instructor office hours

The Instructor, Ira Kalet, is available without prior appointment on Mondays, between 2 and 4 PM, at his office at UW Medical Center. For other times, make an appointment (email works best for making appointments)

Recommended course texts

Kalet, "Principles of Biomedical Informatics"
Graham, "ANSI Common Lisp"

Computing resources

Getting Started [pdf]

Lecture slides and notes

Course introduction from Wednesday, 29-Sep-2010
Computing with molecules from Monday, 4-Oct-2010
Medical images from Monday, 11-Oct-2010
Graphic display systems from Monday, 18-Oct-2010
Safety analysis from Monday, 25-Oct-2010
Network history and principles from Monday, 25-Oct-2010. Note, the socket code demonstrated on Wed, Oct 27 is available at the Common Lisp code web page - the two files are named "sockets.cl" and "examples.cl".
The DICOM network protocol from Monday, 1-Nov-2010
Drug interactions and Information retrieval from Monday, 8-Nov-2010 and Wednesday 10-Nov-2010
Natural Language Processing slides from Meliha and from Ira from Monday, 29-Nov-2010
Probability and Logic from Wednesday, 1-Dec-2010
Information Theory and Nuclear War from Monday, 6-Dec-2010

Slides on Lisp are on the Common Lisp information page, accessible from the main course page.

Reading assignments

Reading assignments should be completed by the indicated class date, in order to be prepared for class. Some of the readings are available through the UW Electronic Course Reserves (Eres) system, at the HONORS 396C page. The initials "PBI" refer to the course text, "Principles of Biomedical Informatics"

For Monday, Oct. 4:
- PBI Chapter 1, Section 1.1.1 and 1.1.2
- PBI Chapter 5, Section 5.3
For Monday, Oct. 11:
- PBI Chapter 1, Section 1.1.5
- PBI Chapter 9, Sections 9.1, 9.2, 9.3.1
For Wednesday, Oct. 20:
- PBI Chapter 10, Sections 10.2 and 10.3 (available at Electronic Course Reserves)
- Therac-25 article at Electronic Course Reserves
- Jon Jacky's article on safety critical computing
For Monday, Oct. 25:
- FDA Advisory on security patches at Electronic Course Reserves
- Jon Jacky's article on formal analysis of the CNTS control program.
For Wednesday, Oct. 27:
- PBI Chapter 8, Sections 8.1, 8.2 and 8.4 (available at Electronic Course Reserves)
For Wednesday, Nov. 10:
- PBI Chapter 7, up to and including Section 7.1 (available at Electronic Course Reserves). Also, please choose two or three familiar drugs, look them up in one or more online resources, to find what you can about their potential interactions with each other. Come to class on Wednesday prepared to report on your experience. No written work to be turned in.
For Monday, Dec. 6:
- Two articles from Communications of the ACM: Alan Borning, "Computer System Reliability and Nuclear War", February 1987, vol. 30, number 2, and David Parnas, et.al., "Evaluation of Safety-Critical Software", June 1990, vol. 33, number 6. To think about: Parnas et.al. write "There is no inherent reason that software cannot be used in certain safety-critical applications...". Are nuclear weapons and ballistic missile systems among these? Why or why not?

Homework

Homework assignments are listed here. Unless otherwise noted, homework is due by the beginning of class on the due date.

Project

It is never too early to begin working on the term project.

Please write a paragraph or two (no more than half a page) describing your (tentative) project idea, and submit it by Monday, October 18 for review and approval.
For Wednesday, November 10, please turn in a project report outline, with a sentence or two describing the project goals, methods and timeline.