MEBI 550: Winter 2010 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.
- Kalet, Principles of Biomedical Informatics
(required), referred to below and in other course documents as
"PBI". As the author, I receive a small royalty on each book. I
have established an endowed fund at the UW, the Ira and Terry Kalet
Fund for Biomedical Informatics Trainees, using this royalty
income. Future royalties will also go into this fund, not retained
by me personally.
- Graham, ANSI Common
Lisp (required), referred to as "Graham".
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
- Search methods, strategies and
- 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,
- Description Logics
- Probability and reasoning under
- Information theory
- Machine learning
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 Tuesday, January 26
(revised from earlier).
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, and
some files from raatkirani, the I-lab Linux server.
- Homework 2, due Tuesday, February 2.
- Homework 3, due Tuesday, February 16.
No programming this time, just proofs.
- Homework 4, due Tuesday, March 2.
- Homework 5, due Thursday, March 11.
Solutions to Homework
Solutions will be emailed
This year, instead of a final exam, students will be expected to do
projects, and submit written reports.
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).