MEBI 531: Life and Death Computing

Instructor: Ira J. Kalet, Ph.D.
Professor, Radiation Oncology
Professor, Medical Education and Biomedical Informatics
Adjunct Professor, Computer Science and Engineering, and Biological Structure

Office: NN146A University of Washington Medical Center

email: ikalet@u.washington.edu

Telephone: (206) 598-4107

Course description

MEBI 531 addresses the complex software design issues that come up in biomedical and health informatics, programming for safety critical applications in medicine and health care, as well as in the application of computing to unlock the secrets of life. Examples from biology, medicine and health motivate software engineering topics such as: use of abstraction layers, design of tightly coupled but modular and extensible software, formal models and safety in real time control of medical equipment, design of network application protocols, integration of diverse biomedical data sources. Many of the examples will use the Common Lisp programming language, but prior knowledge of Lisp is not assumed. The course introduces programming in Common Lisp as well as concepts and methods useable in most programming languages and environments. If time allows the Prolog programming language will also be introduced and used.

Grading and other policies

Answers to frequently asked questions (FAQ)

Current quarter information

The Current quarter information page provides links to homework assignments and other useful information for the current quarter.

Prerequisites

The course assumes previous programming experience at the level of UW CSE 142 Computer Programming I. However, it is not important which programming language you know, as long as you are experienced with at least one. In addition, the course requires certain basic computing skills and mathematical background. These are listed on the Prerequisites page.

Course learning objectives

A list of course learning objectives illustrates what students are expected to be able to know and do by the end of the course.

Web resources on biomedical informatics projects

The UW Structural Informatics Group has a project, the Foundational Model of Anatomy, that captures knowledge about human anatomy in a rich ontology.
The Pacific Symposium on Biocomputing is an annual conference with a published proceedings of high quality papers.
The Unified Medical Language System is a very large lexicon of medical terms and relationships between them.
The PharmGKB project is building an ontology for drugs and genetic variations related to drug responses in individuals.
The Center for Computational Pharmacology at the University of Colorado has a range of interesting projects modeling biomolecular pathways and analysing gene expression data.
The Children's Hospital Informatics Program at Harvard has developed software for a variety of bioinformatics projects.
BioCyc is a collection of Pathway/Genome knowledge resources that each provides a description of the genome and metabolic pathways of an organism. At present 160 organisms are covered.
The Pathway Tools Information Site has information on how to use the Pathway Tools software with the BioCyc databases. There is a link on this page to instructions for using the Lisp API.
Jeff Shrager has written a nice discussion of how to compute dynamic pathways from a simple representation of molecules and reactions similar to that of BioCyc.
The Gene Ontology project, which has constructed a hierarchical classification system representing knowledge about gene products according to molecular process, cellular function and cellular component.

Web resources on Lisp

Some links for more information on Common Lisp and related topics are on the Common Lisp information page

Information from previous quarters

In previous years, the course has focused almost entirely on learning to program in Common Lisp, without assuming any previous programming experience. Starting in Fall 2003, programming experience is prerequisite and the course content has been adjusted accordingly.

Information from previous years is at the following links (the course was not offered in Autumn 2004):