James A. Foster

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Computational Biology

ST: CS 4/504-01 (3 cr)

James A. Foster (foster@cs.uidaho.edu)

Announcement: Be sure to check the materials webpage! Also, there is a notes page, which lecture notes and other stuff.

And here is the syllabus. 


bullet Here is a study guide for the second exam (in pdf).
bullet I have added answer keys for all homework (homework 5, homework 6, and homework 7). Please try to do Homework 7 before looking at the answers, but do see the answers as preparation for the exam.
bullet Class will meet in JEB 26 on 12/13, for student presentations.
bullet I will have open office hours from now until the exam. I will only be unavailable when I'm in a meeting.
bullet There have been significant changes to the schedule. Please see the syllabus.
bullet Homework 7 is available.
bullet We will have only one more examination, the Thursday before deadweek (6 December), and it will not be comprehensive.
bullet Kosuke (one of our students) found the following webpage discussing unsupervised learning.
bullet Homework 3 answers are available online.
bullet First exam will be Thursday, 11 October.
bullet Note: Homework 3 due date is changed to 4 Oct.
bullet I put my Whirlwind tour of bioinformatics online
bullet Check the errata for the O'Reilly textbook
bullet Check here for information on ASN.1 at Genbank, in general

Place and Time 10:30-12:00, Tues. and Thurs., JEB 236


Bioinformatics uses computation and mathematics to interpret biological data, such as DNA or protein sequences or structures.  We already have far more biological data than we can analyze, so we desperately need new algorithms and approaches. 

This course will introduce computational problems posed by biological data, and will introduce the algorithms that have been developed to address them. These are likely to include algorithms for: comparing sequences, database searching, multiple sequence alignment, phylogenetic inferencing. If time permits (and it never does) we will also discuss:  gene discovery and annotation, assembling genomes from sequence data, interpreting DNA array data, and protein structure determination. This is a tentative list, and we may end up exploring just one or two topics in more depth.

The course will be a combination of lectures, projects, and guest presentations. Students will be expected to do team projects, appropriate for their background and interests. Graduate projects will require a class presentation or a paper. I assume either some biology or some computer science background (but not both!).

The objective of this course is to improve interdisciplinary research in bioinformatics and to advance our ability to transform biological data into biological knowledge.  This is part of the mission of the Initiative for Bioinformatics and Evolutionary STudies (IBEST), (see www.cs.uidaho.edu/ibest. For more information, please contact Dr. Foster (foster@cs.uidaho.edu) or see the course webpage

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Last Updated 01/13/2003 15:56 -0800