CAP 5510 (Bioinformatics)

Instructor:	Tamer Kahveci
Email:
Location:	CISE Building E107
Time:	Monday/Wednesday/Friday 8th period (3:00 - 3:50 PM)
Section:	4187
Office hour:	Monday/Wednesday 2:00-2:50 PM
Contact:	E436 (office), 505-1554 (office phone)
TA:	Sanjeev Gadgil (sgadgil @ cise; Office hours: Tue/Thu/Fri 10:45-11:45 AM)

Goals:

This course will discuss the major components of bioinformatics data (such as DNA and protein sequences and protein structures) and how computer technology is used to understand this data better.

Announcements:

Here is the second homework . (11/15/11)
Here is the fifth quiz . (11/09/11)
Here is the fourth quiz . (11/09/11)
Here is the third quiz and the solution . (10/17/11)
You can find class projects here. (10/17/11)
Here is the second quiz and the solution . (09/26/11)
Here is the first homework . (09/19/11)
You can find the course schedule here. (09/12/11)
Here is the first quiz . (09/9/11)
Reading assignment 1: Biological network motif detection: principles and practice. Due August, 29, 2011. You do not need to return anything. (8/24/2011)
Details on project reports are ready. (08/15/11)
Project milestone description is ready. (08/15/11)
You will use Sakai to submit soft copies of your homeworks and check grades. Use your gatorlink login and password for this purpose. (08/15/11)
For EDGE Students: Details on surveys are ready. (08/15/11)
You can find course slides here. (08/15/10)
Here is the course syllabus (08/15/11)
Check the class page regularly for announcements (08/15/10)

Prerequisites:

I will assume that you have already taken data structures and algorithms courses and you are comfortable with basic computer programming (e.g., with C or Java).

Topics:

I am planning to cover the following topics.

Biological sequences
Lossless alignments (different DP problems such as global, local alignment, etc,)
Lossy alignments (BLAST, etc)
Substitution matrices, statistics
Multiple alignment
Phylogeny
Protein structures and function (primary, secondary, etc.)
Structure alignment
Structure prediction
Biological networks

Grading:

Grading will be based on homeworks and quizzes (50 %), project (50 %). EDGE students will return two surveys instead of participation in quizzes. I will reward high quality projects with up to 2.5 % bonus points. 90% or more attendance will be rewarded with up to 2.5 % bonus.

Text book:

I will teach this course from multiple books and some research papers. Therefore, I do not require any textbook. The primary book I will stick to is:

Fundamental Concepts of Bioinformatics by Dan E. Krane, Michael L. Raymer. (ISBN: 0805346333)

For interested students, I recommend the following books as further resources.

Bioinformatics: Sequence and Genome Analysis by David W. Mount. (ISBN: 0879696087)
Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology by Dan Gusfield. (ISBN: 0521585198)
Introduction to Protein Structure by Carl-Ivar Branden, John Tooze.(ISBN: 0815323050)

Other:

Check out disability resources.
Cheating, plagiarism, and other types of academic dishonesty will be subject to punishment.
I encourage class attendence.
Please return your homeworks, project and surveys in time. Late returns will cause 20 % deduction in your grade for that homework (etc) for each late day. Submissions after 5 days from the due date will not be graded.
Please visit only during office hours. If you really need to meet me out of the office hours email me to make an appointment. If I postpone or cancel the office hour, I will post it in the announcements section and (try to) put a note on my office door.
Please avoid any activities that will disturb the flow of the lectures: Silence your cell phones, pagers, etc.

Tamer Kahveci