MEBI 591: BHI Research Colloquium "Advanced Lisp Programming"
J. Kalet, Ph.D.
Professor Emeritus, Radiation Oncology
Professor Emeritus, Medical Education and Biomedical Informatics
MEBI 591 is a one hour per week research seminar, with each section
devoted to a different topic of interest to Biomedical and Health
Informatics and other students. This section, 591A, Autumn 2011, will
focus on advanced programming concepts and their applications in
biomedical computing. The topics will be largely dependent on the
interests of the participants, but likely will include some in depth
discussion of functional programming, object-oriented programming,
metaprogramming, the use of macros to create higher level language
constructs, and how these might be used in solving biomedical
Grading and other policies: this is a CR/NOCR course. Participation
is the key to getting credit. Regular attendance and active
participation will be sufficient to obtain credit. Participation
includes working on a modest programming project and presenting it to
the group for discussion.
The course assumes previous programming experience at the level of UW
CSE 142 Computer Programming I, and some familiarity with Lisp.
Ability to learn quickly is more important than extensive background.
Web resources on Lisp
Some links for more information on Common Lisp and related topics are
on the Common Lisp information page
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
- 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.
Other Web resources
These are some relatively old project links, which are still
interesting as examples of significant applications of Lisp, mostly
focused on knowledge modeling (logic).
- The CYC Project, an attempt to
build an encyclopedic scale system of basic human knowledge in the
form of rules, assertions and other logic forms.
- The Ontolingua
project home page.
- The LOOM
project home page.
- Information about Description Logics
- The Common Logic
standard, which also includes the KIF
language as an instance of a Common Logic.
- The DAML home page.
- The OIL home page.
- The FaCT home page.