San José State University
Computer Science/Biology 123A
Bioinformatics I
Course Code: 48686 for Biol 123A
Course Code: 47614 for CS 123A

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 the biology department, provides an introduction to the main public domain tools, databases and methods in bioinformatics, including DNA and protein databases, such as Genbank and PDB, software tools such as those in the Wisconsin Package, at the National Center for Biotechnology Information (NCBI), and other web accessible applications. More precisely, the course introduces the methods for collecting, editing, and storing macromolecular sequences, for pairwise and multiple sequence alignments, for database searching for similar sequences, and for phylogenetic prediction. This course is intended both for biology and computer science students, to work together to solve complex biological questions requiring the use of standard bioinformatics applications and databases.

Textbook

Textbook Reading Guidelines Last update: May 1, 2009.

Biology Terms

Understanding Bioinformatics by Marketa Zvelebil and Jeremy Baum, Garland Science, 2008, ISBN 0-815-34024-9.
The book can be found at the bookstore under CS123A.

1. We shall cover most of the topics from chapters 1, 2, 3, 4 and 7.
2. Before reaching the end of a chapter, I will announce which topics of the following chapter will be covered.
3. A copy of my powerpoint slides (2 per page and 6 per page) will be available at the Blackboard Learning System (blackboard) 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. Please note that OR in the last sentence is exclusive. In other words, DH450 is never a lecture room AND a computer lab at the same time.
   
   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 (workstation) and do not talk to your classmates. Do not open your laptops. If you are addicted to checking mail, chatting, surfing the internet, etc..., and cannot follow these simple rules, please do not enroll in this class.
   

   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.
   

   Tentative Schedule:

   August 25 to September 8: Introduction to Molecular Biology and to Bioinformatics
   September 8 to October 1: Pairwise Sequence Alignment
   October 6 to October 27: Multiple Sequence Alignment
   November 3 to December 1: Phylogenetic Inference
   
   

2. Problem Sets:
   Five 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. 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 due on Thursday, September 10, 2009.
   • HW Two due on Thursday, September 24, 2009.
   • HW Three due on Thursday, October 15, 2009.
   • HW Four due on Thursday, November 5, 2009.
   • HW Five due on Thursday, November 19, 2009.
     Cover sheet for all assignments
     

3. Term Project:
   There will be a group project. Each group consists of two students. Information on the project is posted at blackboard. The Team Formation is due on Tuesday, October 13, 2009. The Progress Report is due on Thursday, November 12, 2009 at the begining of the class. The final project is due on Thursday, December 3, 2009 at the beginning of the lecture.

4. Exams:
   Exam One: Tuesday, October 6, 2009.
   Exam Two: Tuesday, November 17, 2009.
   Final Exam: Tuesday, December 15, 2009, from 7:15 to 9:30am.
   

   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. Make-up exams will be given only at the instructor's discretion.

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 September 11, 2009. The last day to drop with a full refund is September 3, 2009. According to University and Department guidelines, dropping after September 3, 2009, 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

Students should read the ``Policy on Academic Integrity" in the University Catalog. Anyone caught cheating (including copying the work of others) on any assignment in the class will receive a failing grade for the assignment, in addition to other sanctions that are permitted by the University, including but not limited to the filing of a report with the Dean of Student Services and expulsion from the University. Students should read the ``Policy on Academic Integrity" in the University Catalog. The "Policy on Academic Integrity" can be found here.

• Anyone caught cheating (including copying the work of others) on any assignment in the class will receive a failing grade for the assignment, in addition to other sanctions that are permitted by the University, including but not limited to the filing of a report with the Dean of Student Services and expulsion from the University.
• Your own commitment to learning, as evidenced by your enrollment at San José State University, and the Universitys Academic Integrity Policy requires you to be honest in all your academic course work. Faculty are required to report all infractions to the Office of Judicial Affairs.

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 me as soon as possible, or see me during office hours. Presidential Directive 97-03 requires that students with disabilities register with DRC to establish a record of their disability.

Summer 2010 Internships and Research Programs (Most updates for 2010 will appear in mid-November)