MEBI 591: BHI Research Colloquium "Advanced Lisp Programming"

Instructor: Ira J. Kalet, Ph.D.
Professor Emeritus, Radiation Oncology
Professor Emeritus, Medical Education and Biomedical Informatics

email: ikalet@u.washington.edu

Course description

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 computing problems.

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.

Prerequisites

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.

Practice exercises

• Practice set 1

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 ontology.
• 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.
• 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.