MEBI 550: Winter 2008 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 as a PDF.

Course texts

• Graham, ANSI Common Lisp (required)
• Kalet, Principles of Biomedical Informatics (forthcoming, draft available at the course Electronic Reserves), referred to below and in other course documents as "PBI".

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 Gary Csorgo (gcsorgo@u.washington.edu), the Informatics Lab Manager.

Lecture slides and notes

This list will be expanded as the course progresses.

• Course introduction
• Biomedical data
• Introduction to Logic
• Search
• Prolog
• Logic based systems
• Medical examples of RBS
• About the Graham inference code
• Probability and Bayes' Rule
• Introduction to Information Theory
• The Halting Problem

Reading assignments

Reading assignments are on the course schedule (see above), at the end of the topic list for each date. They are specified by chapter and section, so for example, PBI 1.2 means Chapter 1, Section 2, in the Principles of Biomedical Informatics draft. 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 550 page.

Homework

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

• Homework 1, due Thursday, January 17.
• Homework 2, due Thursday, February 7.
• Homework 3, due Thursday, February 26.

Final Project

This year, instead of a final exam, students will be expected to do projects, and present them to the class. The time and location for this session has not been scheduled yet.

Here are titles for some projects of students in previous years:

• Building a Knowledge-Based System to Support Patient-Centered Care for Diabetes
• Computational Analysis of the Cell Regulatory Cycle using the BioBike Biological Knowledge Base and Lisp Interface

Here are some ideas for projects that have not been done before:

• Analyze the genome of some interesting species to see whether the frequency of occurrence of an amino acid in the proteins correlates with the number of redundant codons for the amino acids, i.e., do the amino acids with 4 to 6 codons occur more frequently than the ones for which there are only one or two codons?
• Apply the state-machine simulation code in Chapter 8 of PBI to some other gene regulatory or protein interaction network, to see what properties of the network you can predict.
• Build an ontology of some biomedical or health area you are interested in, using any of the existing ontology building tools, e.g., Protege, Ontolingua, LOOM, etc.
• Apply an existing knowledge resource to answer some complex biomedical question, e.g. use the Gene Ontology to classify microarray data as in Jeff Shrager's "intelligent microarray analysis" tutorial.
• Get Wanda Pratt's DynaCat program working and apply it to some additional test cases (see instructor for details).