Textbooks

• Recommended (about half of the course will follow this): An Introduction to Bioinformatics Algorithms (by Neil C. Jones and Pavel A. Pevzner)
• Suggested : Probabilistic Models of Proteins and Nucleic Acids ( by Richard Durbin , Sean R. Eddy , Anders Krogh , Graeme Mitchison )

Prerequisites

Format

The course is lecture-based with regular problem sets and machine problem assignments plus a midterm examination and final examination.

Course Policy and Grading

1. Attendance

Attendance is mandatory, but use common sense if you are sick or have other constraints. Note that attending the lectures is sometimes the only chance for you to learn certain materials as they may not necessarily be in the textbook. This is especially the case for the second half of the course, where we cover topics outside of the textbook.



2. Assignments and late turn-in policy

(Note: The following collaboration policy may be over-ridden by the instructor for specific assignments.) The assignments are designed to ensure that students have a deep and precise understanding of the major algorithms and their implementation, thus the students are required to complete them independently. However, discussion with others is allowed to the extent of helping understand the material. The purpose of student collaboration is to facilitate learning, not to circumvent it. The actual solution must be done by each student alone, and the student should be ready to reproduce their solution upon request. If any substantial discussion happens, every one involved must write down the names of the people that he/she has discussed with and the nature or topic of discussion. In any case, you must exercise academic integrity. See the University Policy on Academic Integrity, especially the section on plagiarism.

Late submission of an assignment would result in a reduced grade for the assignment. An assignment is worth full credit at the the due time and date. It is worth at most 80% credit if submitted up to 3 days (72 hours) after the due time and date. It is worth at most 50% credit if submitted up to 7 days late, and worth no credit if submitted more than a week late.

A student may request an extension of 3 days at most once in the semester. If the extension is granted, the due time and date of that assignment is pushed back by 72 hours for that student. Delays beyond this new deadline are penalized as per the rules above.

A student may request an extension only until the due date and time, not beyond it. Extensions may be requested only in case of emergencies, and granting them is at the discretion of the instructor.



3. The optional extra "1 hour" project

Graduate students who take the course for full credit (i.e., 4 graduate hours) are required to finish a small project. The project should be research oriented, and its topic should be approved by the instructor by October 13, 2009. Students who have not contacted the instructor (by email) about their project topic, by this date, will not be eligible for the extra credit. .



4. Grading

Grading will be based on the following weighting scheme.

• Assignments: 40%
• Midterm: 30%
• Final: 30%