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: EE122H University of Washington Medical Center
Telephone: (206) 598-4107
A Syllabus includes most of the information
here (except for the web resources below) in a single PDF document.
This course 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
Information for Honors 396 Autumn 2010
The HONORS 396 C Autumn 2010 information page
provides links to slides, homework assignments and other useful
information for the Autumn 2010 quarter, when this course was taught.
The course assumes some previous programming experience. However, it
is not important which programming language you know, as long as you
have some experience 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 National Center for
Biotechnology Information (NCBI) is the part of the National
Library of Medicine that creates and maintains GenBank, PubMed,
and many other biomedical information resources.
- The Swiss Institute for Bioinformatics maintains
the ExPASy Proteomics Server web
site, which includes the UniProt/SwissProt protein sequence database
and many other resources on proteins.
- David Baker's web
site provides information about his protein folding research and
two ways in which you can participate, Rosetta@Home and the FoldIt game.
- Valerie Daggett's web
site provides information about her protein folding research
projects, including movie clips of simulations.
- The UW Structural
Informatics Group has a project, the Foundational Model of
Anatomy, that captures knowledge about human anatomy in a rich
- 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
for using the Lisp API.
- 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