MEBI 531: Fall 2005 course information
Check here for homework assignments, course notes, and other
hopefully useful stuff.
Tentative lecture topic schedule
The topics we will cover are tentatively scheduled, though we may slip
or add or substitute other topics. The schedule is available in a PDF version and a PostScript version.
The Informatics computing lab (I-Lab) of the Biomedical and Health
Informatics Graduate Program, located in T-277, Health Sciences
Building, provides a Linux server and desktop systems with a Common
Lisp programming environment. To obtain an account and learn about
access, after registering for the course, contact Laurel Rees
(firstname.lastname@example.org), the Informatics Lab Manager.
Lecture slides and notes
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
MEBI 531 page
- Monday, October 3:
- Graham, chapters 1,2
- article available on course eres page: Thomas
K. Hazlet, Todd A. Lee, Philip D. Hansten and John R. Horn,
"Performance of Community Pharmacy Drug Interaction Software"
- draft Chapter 9 of
"Principles of Biomedical Informatics"
- Wednesday, October 5:
- Graham, chapter 3
- article available on course eres page: Hanlon et.al.
"Suboptimal Prescribing in Older Inpatients and Outpatients"
- article available on course eres page: Kuo, et.al.,
"Guideline Interactions: a study of interactions among
drug-disease contraindication rules"
- Wednesday, October 12:
- Monday, October 17:
- On the Clinical
Neutron Therapy System web page there are two useful links to
review before the cyclotron tour, one of which is an overview of
the control system project ("A control system for a radiation
therapy machine") and the other is about the development
methodology ("Formal safety analysis").
- Wednesday, November 2 and Monday November 7:
- Graham, chapter 17 (requires material also from chapter 4,
namely arrays and hash tables)
- article available on course eres page: Peter Karp,
"An ontology for biological function based on molecular
- document available on course eres page: Peter Karp, et. al.,
"Pathway Tools User's Guide"
- Monday, November 14 and Wednesday, November 16:
- article available on course eres page: Bidgood,
et.al. "Understanding and using DICOM..."
- document available on course eres page: chapters 1 and 12 of
"Principles of Biomedical Informatics" (data and DICOM chapters)
- Monday, December 5 and Wednesday, December 12: articles on
medical guideline formalisms and systems
- "Rationale for the Arden Syntax", George Hripcsak, Peter
Ludemann, T. Allan Pryor, Ove B. Wigertz and Paul D. Clayton,
Computers and Biomedical Research 27, 291-324 (1994)
- "The Asgaard project: a task-specific framework for the
application and critiquing of time-oriented clinical guidelines",
Yuval Shahar, Silvia Miksch, and Peter Johnson, Artificial
Intelligence in Medicine 14 (1998) 29-51
- "Representation primitives, process models and patient data
in computer-interpretable clinical practice guidelines: A
literature review of guideline representation models", Dongwen
Wang, et. al., International Journal of Medical Informatics 68
- "GLIF3: a representation format for sharable
computer-interpretable clinical practice guidelines", Aziz Boxwala,
et. al. Journal of Biomedical Informatics 2004 Jun;37(3):147-61
- "Design and implementation of the GLIF3 guideline execution
engine", Dongwen Wang, et. al., Journal of Biomedical Informatics
37 (2004) 305-318.
- "A framework for a distributed, hybrid, multiple-ontology
clinical-guideline library, and automated guideline-support tools",
Yuval Shahar, et. al., Journal of Biomedical Informatics 2004
Homework assignments are listed here. Unless otherwise noted,
homework is due by the beginning of class on the due date.
- Assignment 1, due Monday, October 10
- Assignment 2, due Monday, October 17
- Assignment 3, due Monday, October 31
- Assignment 4, due Wednesday, November 16
- Assignment 5, due Wednesday, December 7
Solutions to Homework
Solutions will be posted here.
There will be a final exam on Monday, December 12, at 2:30 PM, in our
regular classroom, E216 Health Sciences Building. NOTE: this time is
NOT the same as our regular class starting time.