San José State University
Biology 221T
Advanced Bioinformatics for Biotechnology
Course Code: 49639

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

Bioinformatics applications to solve advanced problems in molecular and cell biology.

Prerequisites

This course is offered to students enrolled in the Master of Biotechnology (MBT) program at San Jose State University. MBT offers an opportunity to develop a profession combining scientific interests with business and management principles relevant to the biotech industry.

Textbook

Discovering Genomics, Proteomics, and Bioinformatics by : A. Malcolm Campbell and Laurie J. Heyer, Pearson Benjamin Cummings, 2007, Second Edition, ISBN 0-8053-8053-4.

1. You will find a wealth of information including links, explanations, definitions, etc... of each chapter at: http://wps.aw.com/bc_campbell_genomics_2/
2. We shall cover most of the topics from chapters 1, 2, 3, and 4, and some selected topics from chapters 8 and 9.
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 textbook every Tuesday to class.
5. A copy of my powerpoint slides (6 per page) will be available to the students enrolled in the class.

Course Objectives

1. Use case studies in in-class hands-on exercises to extract generalizable concepts.
   
2. Understand the nature, scope and limits of the field of bioinformatics.
3. Have a good familiarity with bioinformatics applications used for sequence alignment and gene expression analysis.
4. Know how bioinformatics can be used to answer biological questions and to generate biological hypotheses.
5. Possess a refined sense of the professional form of biomolecular information.
6. Acquaint students with some of the most challenging problems in life science and show how computer science can be used to solve some of these problems.

Course Requirements

1. Hands-On Exercises
   We will have a number of hands-on exercises. The purpose of the hands-on exercises is to develop your understanding of the material.
   
   Dual Role of the classroom, DH550: Lecture/Lab
   The classroom, DH550, is a dual purpose room. It can be a regular lecture room or it can be a computer laboratory.
   
   Lecture Mode: This is when DH550 is used as a regular lecture room. Students are expected to listen and follow the lecture. The classroom is noisy because of the large number of computers. 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 DH550 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).
   
   
2. 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, September 22, 2009. The Progress Report is due on Tuesday, November 3, 2009, at the begining of the lecture. The final project is due on Tuesday, December 1, 2009, at the beginning of the lecture.

3. Exams:
   Exam One: Tuesday, October 6, 2009.
   Exam Two: Tuesday, November 17, 2009.
   Final Exam: Tuesday, December 15, 2009 from 5:15 to 7:30pm .

   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:

Hands-On Exercises: 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 4, 2009. According to University and Department guidelines, dropping after September 4, 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

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.)