San José State University
Computer Science/Biology 123A
Bioinformatics I
Course Code: 48736 for Biol 123A
Course Code: 46943 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: 13:15 to 14:15.

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: September 1, 2011.

Biology Terms

Understanding Bioinformatics by Marketa Zvelebil and Jeremy Baum, Garland Science, 2008, ISBN 0-815-34024-9.
The book can be found at Robert's Bookstore, at 330 South 10th Street, under Biology/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 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 21 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 12, 2013.
   • HW Two due on Thursday, October 3, 2013.
   • HW Three due on Thursday, October 17, 2013.
   • HW Four due on Thursday, November 7, 2013.
   • HW Five due on Thursday, November 21, 2013.
     Cover sheet for all assignments
     

3. Term Project:
   Information on the term project can be found here. It is a group project. Each group consists of two students. As mentioned in the project description, the Team Formation is due by Thursday, September 26, 2013. The Progress Report is due by Thursday, October 24, 2013 at the begining of the class. The final project is due on Tuesday, December 3, 2013 at the beginning of the lecture.

4. Exams:
   Exam One: Thursday, October 10, 2013.
   Exam Two: Thursday, November 14, 2013.
   Final Exam: Thursday, December 12, 2013, 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 10, 2013. The last day to drop with a full refund is September 3, 2013. According to University and Department guidelines, dropping after September 3, 2013, 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.
Students are responsible for understanding the policies and procedures about add/drop, grade forgiveness, etc. Refer to the current semester's Catalog Policies section at http://info.sjsu.edu/static/catalog/policies.html. Add/drop deadlines can be found on the current academic year calendars document on the Academic Calendars webpage at http://www.sjsu.edu/provost/services/academic_calendars/. The Late Drop Policy is available at http://www.sjsu.edu/aars/policies/latedrops/policy/. Students should be aware of the current deadlines and penalties for dropping classes. Information about the latest changes and news is available at the Advising Hub at http://www.sjsu.edu/advising/.

Consent for Recording of Class and Public Sharing of Instructor Material

University Policy S12-7, http://www.sjsu.edu/senate/docs/S12-7.pdf, requires students to obtain instructor's permission to record the course. Common courtesy and professional behavior dictate that you notify someone when you are recording him/her. You must obtain the instructor's permission to make audio or video recordings in this class. Such permission allows the recordings to be used for your private, study purposes only. The recordings are the intellectual property of the instructor; you have not been given any rights to reproduce or distribute the material.
Course material developed by the instructor is the intellectual property of the instructor and cannot be shared publicly without his/her approval. You may not publicly share or upload instructor generated material for this course such as exam questions, lecture notes, hands-on exercises or homework solutions without instructor consent.

Academic Integrity

Your commitment as a student to learning is evidenced by your enrollment at San Jose State University. The University Academic Integrity Policy S07-2 at http://www.sjsu.edu/senate/docs/S07-2.pdf 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 Student Conduct and Ethical Development website is available at http://www.sjsu.edu/studentconduct/. Instances of academic dishonesty will not be tolerated. Cheating on exams or plagiarism (presenting the work of another as your own, or the use of another person's ideas without giving proper credit) will result in a failing grade and sanctions by the University. For this class, all assignments are to be completed by the individual student unless otherwise specified. If you would like to include your assignment or any material you have submitted, or plan to submit for another class, please note that SJSU's Academic Integrity Policy S07-2 requires approval of instructors.

• 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.

Campus Policy in Compliance with the American Disabilities Act

If you need course adaptations or accommodations because of a disability, or if you need to make 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 at http://www.sjsu.edu/president/docs/directives/PD_1997-03.pdf requires that students with disabilities requesting accommodations must register with the Accessible Education Center (AEC) at http://www.sjsu.edu/aec to establish a record of their disability.
In 2013, the Disability Resource Center changed its name to be known as the Accessible Education Center, to incorporate a philosophy of accessible education for students with disabilities. The new name change reflects the broad scope of attention and support to SJSU students with disabilities and the University's continued advocacy and commitment to increasing accessibility and inclusivity on campus.

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