MEBI 550: Winter 2009 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.
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
(email@example.com), the Informatics Lab Manager.
Lecture slides and notes
This list will be expanded as the course progresses.
- Course intro, with a little
about biomedical data representation.
- Biomedical data, tagged data, databases
- Logic intro, propositional logic,
and implementation of a theorem prover
- First Order Logic,
introducing variables and quantifiers
- Expert systems, medical
examples, guideline systems
- Alternatives to First Order Logic,
- Search methods, strategies and
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
"Principles of Biomedical Informatics". 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
Reserves (Eres) system, at the MEBI 550 page.
Homework assignments are listed here. Unless otherwise noted,
homework is due by the beginning of class on the due date.
- Homework 1, due Monday, January 12.
You will need code from PBI, Chapter 1, available at the PBI web
page or the Common Lisp code page on the course web site. You will
also need the data file, brca1.txt.
- Homework 2, due Monday, January 26.
- Homework 3, due Monday, February 2.
- Homework 4, due Monday, February 9.
- Homework 5, due Monday, March 2.
Solutions to Homework
Solutions will be emailed
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
- 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?
Here are some ideas for projects that have not been done before:
- 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
- Get Wanda Pratt's DynaCat program working and apply it to some
additional test cases (see instructor for details).