CS 6670

CS 6670: Advanced Bioinformatics

Instructor: Charles Yan

Email: cyan@cc.usu.edu

Office: Old Main 401F

Phone: 797-2570

Place: Old Main 121

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.

Quizzes:

Quizzes will be given at the beginning of a class without a notification in advance. A quiz will cover the materials taught in the previous class.

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%
Quizzes 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% reduction in score. Assignments overdue by more than three days will get a grade of 0, 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:

If a student has a disability that will likely require some accommodation by the instructor, the student must contact the instructor and document the disability through the Disability Resource Center, preferably during the first week of the course. Any requests for special considerations relating to attendance, pedagogy, taking of examinations, etc. must be discussed with and approved by the instructor. In cooperation with the Disability Resource Center, course materials can be provided in alternative formats, e.g. large print, audio, diskette, or Braille.

Last day to Drop Without Notation: 17^th September.

Last day to Add: 17^th September.

Class Schedule:

Aug 27: Introduction

Aug 29 Motifs and Matching (Slides)

Sep 5 Preprocessing (Slides)

Sep 7-14 Boyer-Moore (Slides)

Sep 17- Sep 26 Exact set matching (Slides)

Sep 28-Oct 12: Suffix trees (Slides)

Oct 15, 17, 22: Final projects introduction (Slides_MC, Slides_PST, Paper, Discussion)

Oct 24- Nov 9: Suffix trees (Applications)

Nov 11-Nov 30: Inexact matching (Alignments, motif_scanner, graph kernels)