CPT S 471/571: COMPUTATIONAL GENOMICS

SPRING 2011

(JAN 10 - May 6)
SCHOOL OF EECS
WASHINGTON STATE UNIVERSITY

MW  16:15:17:30
TERR 24 (Pullman campus)

Course Information        Policies      Lecture Notes        Course Schedule        Homeworks        Programming Projects        Survey Project    (old announcements archive)

CURRENT ANNOUNCEMENTS

• Link for the survey project is now active (see link above)
• Program 3 posted below
• HW3 posted below

COURSE INFORMATION

Instructor:

ANANTH KALYANARAMAN

EME 237, 335-6760

Weekly office hours:  By appointment

Instructor email contact: Through the Angel system

Reference texts

•     Handbook of Computational Molecular Biology, Srinivas Aluru (Editor), 2005, ISBN: 1584884061
•     Biological Sequence Analysis: Probabilistic Models of Protein and Nucleic Acids, Durbin et al. 1999, ISBN: 0521629713
•     Algorithms on strings, trees and sequences: Computer Science and Computational Biology, Dan Gusfield, 1997, ISBN: 0521585198

Course Webpage & the Angel Portal:

    The course will use two web resources for two different purposes:

• The "course website" (i.e., this page you are reading now) is where lecture notes, all assignments will be posted, and the course schedule will be maintained.
• The ANGEL web portal will be used for email exchanges, email announcements, and listing of useful web links/resources.
   All email correspondences with the instructor should be sent through the Angel . Please do not use personal email ids to send from or send to the instructor, as they will be discarded.

        Angel home:    http://angel.wsu.edu/

        Angel login page:    https://lms.wsu.edu/

        Angel "Getting Started" link:    http://angel.wsu.edu/GetStarted.asp

• Mail Alert:    Students are advised to check their ANGEL mailbox at least once a day.

Course Prerequisites:

• Familiarity with design and analysis of algorithms is required (CptS 450 or equivalent).
• Familiarity with basic probability concepts
• NO prior background in biology is assumed. Basic concepts required to understand and appreciate the importance of a problem will be described on a need-to-know basis, while the primary emphasis will be on the design of algorithmic techniques and applying them on real data.
• Programming experience in one of the following programming languages is required: C, C++, Java. If you know Perl or Python that may be OK too, but please talk to the instructor if that is the case.

 Interested students who do not meet the above criteria are highly encouraged to contact the instructor to discuss the possibility of enrolling into the course.

COURSE POLICIES

Grading policy:

For Cpt S 571 students:

• (32.5%) 3  homeworks
• (32.5%) 3 programming projects
• (20%) 1 midterm exam
• (15%) survey project

For Cpt S 471 students:

• (35%) 3  homeworks
• (40%) 3 programming projects
• (25%) 1 midterm exam

Collaboration policy:  All assignments are individual assignments unless explicitly stated otherwise in the assignment. Collaboration may be allowed on a selected part of an assignment and it will be explicitly stated if that is the case. In such cases, strict adherence to the following guidelines is required:

• "Collaboration" is defined as a discussion with other students in the same class (no outsiders allowed) aimed at obtaining a better understanding of the problem question and/or exploring potential approaches at a very high level that can lead to a solution.
• All collaborative efforts should be explicitly acknowledged/cited in the answer sheet by all the participants using the cover sheet.
• Regardless of whether you collaborate or not, the final writing in the answer sheet should be solely yours.
• No points will be deducted for collaboration as defined above.
• Any deviation from the above guidelines will be considered "cheating" and will be subject to academic dishonesty code. This includes sharing or showing your solutions with others in the class. Also, looking up solutions on the web should be strictly avoided and if evidence is found, it will be considered cheating.

        Academic Integrity Policy (please read)

Late submission policy:

• No late submissions will be allowed on any assignment
• Extensions may be allowed under extraordinary circumstances upon obtaining prior permission from the instructor, at least 1 week prior to the submission date. Last minute permissions will not be typically allowed.

Exam policy: Closed-book, closed-notes, comprehensive

HOMEWORKS

• Homework 1 PDF
• Homework 2 PDF
• Homework 3 PDF

PROGRAMMING PROJECTS

• Program 1 HTML
• Program 2 HTML
• Program 3 HTML

Click here to download the cover sheet for use in all the homeworks and programming projects (same for both 471 and 571 students).

SAFETY ON CAMPUS

http://alert.wsu.edu

WSU Campus Safety Plan:    http://safetyplan.wsu.edu/

Get familiar with the emergency procedures from the above links.

STUDENTS WITH DISABILITIES

DRC website:    http://www.drc.wsu.edu

Reasonable accommodations are available for students with a documented disability. If you have a disability and may need accommodations to fully participate in this class, please visit the Disability Resource Center (DRC). All accommodations MUST be approved through the DRC (Admin Annex Bldg, Room 205). Please stop by or call 509-335-3417 to make an appointment with a disability specialist.Visit the DRC website for more information.

OLD ANNOUNCEMENTS ARCHIVE

• Program 2 posted
• HW2 posted
• Program 1 posted
• Cover sheet can be downloaded from the link below homeworks and programming projects
• HW1 posted
• Please make sure you can login to Angel and see my welcome email message. If not immediately contact Angel Helpdesk and get it fixed.
• Welcome to the Cpt S 471/571 class of Spring 2011.

COURSE ARCHIVES

Spring 2007, Spring 2008, Spring 2009, Spring 2010