CS 6670

CS 6670: Advanced Bioinformatics

Instructor: Charles Yan

Email: cyan@cc.usu.edu

Office: Old Main 401F

Phone: 797-2570

Place: Old Main 117

Time: MWF 3:30 pm - 4:20 pm

Office Hours: MWF 2:00 pm-3:00 pm

Course Goals:

Understand the details in algorithm design and model building in bioinformatics.
Become familiar with the design and development of the algorithms and models.
Realize the advantages or disadvantages of the various approaches.

Learning Outcomes:

Have a sufficient background for research in bioinformatics.
Be able to apply the algorithms and models to solve real bioinformatics problems.

Assignments:

Assignments will be given throughout the class at the pace of one assignment two weeks.

Exams:

None.

Final Project:

Students are encouraged to work in a team of no more than three persons. You are expected to do exploratory experiments on a topic in bioinformatics.

Grading:

Assignments 50%
Class participation 10%
Final project 40%

Late Work:

Assignments are due at midnight on the due date. Assignments handed within three days after the due time will be subjected to a 25% penalty in score. For example, if the total score of the assignment is 100 points, then 25 points will be reduced from whatever the student has. Assignments overdue by more than three days will get 0 point, except for a legitimate reason, e.g. illness, which must be documented.

Course Website:

The website for this course is http://www.cs.usu.edu/~cyan/CS6670/. Homework and lecture notes will be posted on the site.

Textbook:

Algorithms on strings, trees, and sequences By Dan Gusfiled, Cambridge University Press, ISBN 0-521-58519-8

Code of Conduct for Computer Science Classes:

As a computer scientist, or someone taking a computer science class, you are expected to perform your work at all times in an ethical manner. This means that in addition to doing your own work and giving appropriate credit when the work of others is used, you are required to protect your work.

A student that protects their work will not allow another student access to that work whether it be allowing it to be copied, or treating its security in such a way as to give unintentional access, such as "accidental" loss. It is the policy of the department that when duplicate (essentially the same) work is turned in by two or more students, without acknowledgement of allowed cooperation, all involved students will be considered in violation of this department policy. Under such circumstances, each student will receive minus the points possible for the work.

Thus, for a 15 point assignment, all would receive -15 points. If the infraction is deemed more egregious, then further action may be taken.

ADA Compliance:

Students with ADA-documented physical, sensory, emotional or medical impairments may be eligible for reasonable accommodations. Veterans may also be eligible for services. All accommodations are coordinated through the Disability Resource Center (DRC) in Room 101 of the University Inn, (435)797-2444 voice, (435)797-0740 TTY, or toll free at 1-800-259-2966. Please contact the DRC as early in the semester as possible. Alternate format materials (Braille, large print or digital) are available with advance notice.

MSDNAA note:

The Computer Science Department is a member of the Microsoft Academic Alliance (MSDNAA), and specifically what is now called the Developer Academic Alliance. Through this program, students in CS courses can obtain and use a large number of Microsoft's operating systems and software packages. If you are interesting in downloading any of this software for your use, please follow the directions found at http://www.cs.usu.edu/elms.html

Last day to Drop Without Notation on Transcript: 15^th September.

Last day to Add: 15^th September.

Grader

Juan Shan (juan.shan@aggiemail.usu.edu)

Class Schedule:

Aug 25 Introduction

Aug 27 Matching problems in bioinformatics

Aug 29 Preprocessing

Sept 10 Boyer_Moore

Sept 22 Set matching

Oct 3 Suffix Trees

Oct 3 Applications of Suffix Trees