Computer Science 426: Introduction to Bioinformatics
Spring 2007

Tue, Thu 1:25-2:40 at Upson Hall 109

Announcements

• 5/3 – You can bring with you to the final a single one sided letter style page (8.5X11) as well as a calculator that has absolutely no programming nor advanced storage capability.

• 4/25 – HW #6 is now available through CMS. Its due date is May 11^th.

• 3/29 – HW #4 is now available through CMS. Its due date is April 10^th.

• 3/9 – HW #3 is now available through CMS. Its due date is March 27^th.

• 2/22 – HW #2 is now available through CMS. Again, it's rather long so start working on it before its due date of March 6^th.

• 2/6 – HW #1 is now open through CMS. It's long so don't wait for the last minute!

• 1/25 – Today's notes are available through CMS.

• 1/24 – Yesterday's lecture notes are available through CMS. To log in you need your netID. Please email me your netID if you do not see the course listed among your courses or if you can't log into the system.

Staff

• Instructor: Uri Keich, 4159 Upson Hall, 5-7017 <keich@cs>

• Teaching Assistant: Ravikant Dintyala, 227-6707, Upson Hall 316 <ravid@cs>

• Administrative assistant: Cindy Robinson, 4146 Upson Hall, 5-0985, <cindy@cs>

Office Hours (or by email appointment)

Books (on hold in the Engineering Library)

• Genomes / T.A. Brown

• An introduction to bioinformatics algorithms / Neil C. Jones, Pavel A. Pevzner

• Biological sequence analysis : probabilistic models of proteins and nucleic acids / Richard Durbin et al.

• Statistical methods in bioinformatics : an introduction / Warren Ewens, Gregory Grant.

Syllabus

A draft syllabus is contained in the notes of the first class. Deviations are expected but it does give the big picture.

Prerequisites

Nothing written in stone, but the following concepts will be used with minimal or no explanations: trees, algorithms, complexity, basic probability (terms such as distribution and density functions, binomial random variable, expectation). You should also be able to program at least in a scriptable language such as Matlab or Perl.

Final

There will be a final on Friday May 11, 2:00-4:30pm in Hollister 372.

Homework

There will be biweekly homework sets, generally due on Tuesdays. Homework should be handed in class just before it starts on the day it is due.

Late homeworks will not receive credit. (If a genuine emergency situation prevents you from handing in an assignment on time, come talk to me and we can work something out.)

You are allowed to collaborate on the homework to the extent of formulating ideas as a group. However, you must write up the solutions to each problem set completely on your own. You must also list the names of everyone that you discussed the problem set with.

Grade Breakdown

The overall course grade will be determined as follows: 60% based on the final exam and 40% based on the cumulative homework score.

Academic Integrity

You are expected to maintain the utmost level of academic integrity in the course. Any violation of the code of academic integrity will be penalized severely.

You are allowed to collaborate on the homework to the extent of formulating ideas as a group. However, you must write up the solutions to each problem set completely on your own. You must also list the names of everyone that you discussed the problem set with.