San José State University
Computer Science/Biology 123B
Bioinformatics II
Course Code: 28834 for Biol 123B
Course Code: 26822 for CS 123B

Link to biotechnology companies in the Bay Area.

Information about the Instructor

Name: Sami Khuri
Office: 418 MacQuarrie Hall
Phone: 924-5081
Office Hours: Tuesdays and Thursdays: 10:20 to 10:45 and 13:20 to 15:00.

Catalogue Description

This practical course, cross-listed with biology, continues to cover the computational methods used for searching, classifying, analyzing, and modeling protein sequences. The course also continues to cover tools for analyzing DNA and RNA sequences. More advanced topics, such as genetic algorithms and simulated annealing which can be used to address folding problems, are covered.

Prerequisites

Biology/CS123A or by permission of the instructor.

Textbook

Biology Keywords

Introduction to Bioinformatics by Arthur Lesk, Oxford University Press, Second Edition 2005.

1. We shall continue covering most of the topics from chapters 2, 3, and 4, and some selected topics from chapters 5 and 6.
2. Please note that the book contains a few subsections on Perl with some sample code. We are not at all going to cover these sections. Any student interested in Perl is encouraged to enroll in CS 122 which will be taught in the Spring 2008 semester.
3. Before reaching the end of a chapter, I will announce which topics of the following chapter will be covered cover.
4. Please bring the book to every class meeting.
5. A copy of my powerpoint slides (6 per page) will be available to the students enrolled in the class.

Course Objectives

Course Requirements

1. Dual Role of DH450: Lecture/Lab
   DH450 is a dual purpose room. It can be a regular lecture room or it can be a computer laboratory.
   
   Lecture Mode: This is when DH450 is used as a regular lecture room. Students are expected to listen and follow the lecture. DH450 is a noisy room because of the large number of workstations and the server. Be considerate to your classmates and follow the lecture. Do not use the computer and/or talk to your neighbor.
   Lab Mode: This is when DH450 is used as a computer lab. Use the computers and share your ideas and solutions with your classmates.
   
   We shall alternate between the two modes. A typical class will begin with a short lecture (Lecture Mode) followed by a hands-on (Lab Mode). We will have a number of hands-on exercises. The purpose of the hands-on exercises is to develop your understanding of the material.
   
   
2. Problem Sets:
   Four homework assignments. The purpose of the assignments is to develop your understanding of the material and your skills in problem-solving. Only a subset of the assigned problems on any given problem set will be graded. You will get the homework back one week after submitting it. No late homework will be accepted. However, under exceptional circumstances, one problem set per student might be accepted late. It will need to be handed in prior to the following class meeting and will be graded with 30% off. Such an extension should be requested from the instructor. Any homework not picked up during class time will be left on the shelves near my office door. Assignments are due in the beginning of the lecture on the following dates:
   • HW One: HW One: Thursday, February 14, 2008.
     Article: A vision for the future of genomic research article for Problem 3.
     Article: Gene regulation in hematopoiesis: new lessons from Thalassemia for Problem 6.
     
   • HW Two: Thursday, March 13, 2008.
     Article: How do RNA folding algorithms work? for Problem 1.
     
   • HW Three: Thursday, April 10, 2008.
   • HW Four: Thursday, May 1, 2008.
   
   Cover sheet for all assignments

3. Term Project (Updated on April 18, 2008).
   There will be a group project. Each group consists of two students. Information on the project will be given in class. The final project is due on Thursday, May 8, 2008, at the beginning of the lecture.

4. Exams:
   Exam One: Tuessday, March 4, 2008.
   Exam Two: Tuesday, April 29, 2008.
   Final Exam: Thursday, May 15, 2008, from 7:15 to 9:30 am.

   Exam One and Exam Two are each one hour and fifteen minutes long. All exams are in-class, closed-book and comprehensive. You will get back your exams within one week at which time we'll go over them in class. Exams will be collected and kept with me. There will be no make-up exams.

Class Attendance

Class attendance is strongly encouraged. In class, we shall cover many topics and examples that are neither in the class notes nor in the textbook. If you miss a lecture, it is your responsibility to find out what was covered in class (this includes: handouts given out during your absence, corrected typos and errors, examples discussed in class - that are neither in the book nor in the notes - clarifications and changes made to assignments or the project, etc...).

Grading Policy

The final grade will be computed as shown below:

Assignments: 20%
Exam One: 20%
Exam Two: 20%
Project: 10%
Final: 30%

[97, 100] A+
[93, 97) A
[90, 93) A-
[87, 90) B+
[82, 87) B
[80, 82) B-
[77, 80) C+
[72, 77) C
[70, 72) C-
[67, 70) D+
[62, 67) D
[60, 62) D-
[0, 60) F

Add/Drop Policy

For those wishing to add this course, the deadline is February 11, 2008. The last day to drop with a full refund is February 4, 2008. According to University and Department guidelines, dropping after February 4, 2008, requires a serious and compelling reason to drop a course. Grades alone do not constitute reason to drop a course. Students who stop attending without officially dropping will be issued a U at the end of the semester which is counted as an F in calculations of GPA. See University Catalog.

Academic Integrity

Your own commitment to learning, as evidenced by your enrollment at San José State University, and the University's Academic Integrity Policy requires you to be honest in all your academic course work. Faculty members are required to report all infractions to the Office of Student Conduct and Ethical Development. The "Policy on Academic Integrity" can be found here.

Disability Resource Center

If you need course adaptations or accommodations because of a disability, or if you need special arrangements in case the building must be evacuated, please make an appointment with us as soon as possible, or see us during office hours. Presidential Directive 97-03 requires that students with disabilities requesting accommodations must register with DRC to establish a record of their disability. (Please let us know as soon as possible in order to more effectively accommodate your needs.)

Summer 2008 Internships and Research Programs