CS 329E: Elements of Computing: Algorithms for Bioinformatics

Instructor: Tandy Warnow

TuTh 3:30-5:00, JES A305A

Office Hours: Wednesdays, 3-4 PM, in ACES 3.428 (and by appointment)

Are you interested in biology, but don't know much about it? Would you like to know how biologists use software to answer deep biological questions? Would you like to learn how to design algorithms, but don't know how to program? Do you like to program, and would you have fun designing programs that can analyze DNA sequences and discover interesting things?

If you answered yes to any of these questions, this course may be just for you! This course will introduce you to the modern world of bioinformatics, covering not only basic biology (in a very easy way, don't worry!), but also how to design algorithms, what it means for a problem to be "NP-hard" and how to deal with that, and how biologists put all these things together to make powerful software that can shed light on fundamental problems. If you know how to program (for example, if you've already taken the Elements courses that are pre-requisite to this course), you'll be able to apply that skill to some interesting problems. If you don't know how to program, you can still take the course! I'm organizing this so that everyone who's interested in this area will have a blast. Feel free to contact me if you have questions! I read email regularly.

The grading scheme is:

Class participation: 10%
Class presentation: 10%
HW: 30%
Quizzes: 30%
Final: 20%

Textbook: An introduction to Bioinformatics Algorithms, by Neil C. Jones and Pavel A. Pevzner, MIT Press.

Homework Policy

You may work in groups of three, but you must write up the solutions to the homeworks yourself.

Additional Notes

Course material may vary depending on student interest.

Academic honesty:

Please see Professor Elaine Rich's discussion of academic honesty and appropriate conduct.
Most importantly, do not, under any circumstances, submit work that is not your own work. Penalties for cheating are very serious, and cheating becomes part of your permanent university record.

Syllabus

Downloadable materials, here. This page gives lectures (in pdf and powerpoint), homework assignments, and class notes.

Announcement: I have tried, but not been able to obtain another classroom; all available classrooms are too small for the class. I'm sorry!

Announcements

First Quiz, February 12th. Topic: running time, big-oh analyses, solving recurrence relations, induction, and using oracles to solve problems. Full credit will be given for solutions that only use a polynomial amount of operations (where oracle calls are single operations).

Office hours for Professor Warnow on April 1 are cancelled (this is not an April Fool's joke), because she will be out of town.

The textbook is reportedly available in the bookstore.