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.

Course text

• Graham, ANSI Common Lisp

Computing resources

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 (lrees@u.washington.edu), the Informatics Lab Manager.

Lecture slides and notes

• Course introduction
• Introduction to Common Lisp
• Drug Interactions
• Software Safety
• The Common Lisp Object System (CLOS)
• Computer Network Concepts
• The DICOM Medical Image Transmission Standard
• Introduction to Natural Language Processing
• Introduction to Prolog
• A little about the Graham inference code

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 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:
  • Safety Critical Computing article by Jonathan Jacky
  • article on the Therac 25 accidents Nancy G. Leveson and Clark S. Turner, "An investigation of the Therac-25 accidents", IEEE Computer, 26 (7): 18--41, July 1993.
• 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 interactions"
  • 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 (2002) 59-70.
  • "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 Oct;37(5):325-44.

Homework

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.

• Solutions for Assignment 1
• Solutions for Assignment 2
• Solutions for Assignment 3
• Solutions for Assignment 4

Final Exam

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.