San José State University
Computer Science 223
Bioinformatics

Fall 2008
Tuesdays and Thursdays: 12:00 to 1:15 in MH223
Course Code: 47647


Helpful links

For those of you who would like to have a head-start:

Remark

Biology is not a prerequisite for this course. But an interest in Biology is. I will spend the first 4 lectures of the course going over some notions in biology (mainly the following Biology Terms) that will be needed for the course.

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.

Catalog Description

The course investigates the main algorithms for solving computational problems in bioinformatics. Methods will include Hidden Markov Models for gene prediction and protein profiling, and Genetic Algorithms for biological sequence analysis and structure prediction. Students will be given programming projects. The course is self contained and does not assume any background knowledge in biology. Students will be given programming projects.

Prerequisite: CS123A or CS155 or permission of the instructor.

Remark

Biology is not a prerequisite for this course. But an interest in Biology is. I will spend the first 4 lectures of the course going over some notions in biology (mainly the following Biology Terms) that will be needed for the course.

Recommended Textbooks (Not required)

Introduction to Computational Molecular Biology by J. C. Setubal and J. Meidanis. PWS Publishing Company, Boston, 1997.
Bioinformatics and Functional Genomics by Jonathan Pevsner, John Wiley, 2003.

Course Objectives

  • Become familiar with problems from computational biology and their solutions. The main emphasis is on algorithms. Most problems are computationally very difficult, therefore, we will examine exact, approximation and heuristic algorithms.
  • Become proficient in bioinformatics software and public WWW resources.
  • Acquire the ability to read scientific papers related to the bioinformatics field.
    Upon successful completion of this course, students should be able to use dynamic programming for pairwise alignment and RNA structure prediction, to know various algorithms for multiple sequence alginment, to have a clear understanding of how hidden Markov models are used for gene prediction, for protein profile construction, and for pattern recognition techniques in general, to understand various phylogenetic tree algorithms, and to know various databases for DNA and protein sequences.

    Course Requirements

    Tentative Schedule:

    Weeks one and two: Introduction to Molecular Biology and to Bioinformatics
    Weeks three and four: Pairwise and Multiple Sequence Alignments
    Week five: DNA Fragment Assembly including NP-Completeness
    Weeks six and seven: Hidden Markov Models
    Weeks eight and nine: Protein Profiling, Gene Prediction
    Weeks ten and eleven: Phylogenetic Inference
    Week twelve: Genome Rearrangement
    Week thirteen: RNA Secondary Structure Analysis
    Week fourteen: Genetic Algorithms for Protein Structure Prediction.

    Problem Sets:

    Five homework assignments. Only a subset of the assigned problems will be graded (per homework), and you will get back the homework a week after submitting it. No late homework will be accepted. The assignments are due in the beginning of the lecture, on the following dates:
    Cover sheet for all assignments

    Term Project

    Information on the group project can be found here. Each group consists of two students. The group chooses a topic, writes a term-project, and gives an in-class, 20 minute presentation (10 minutes per student) at the end of the semester during class time (dates to be announced later in the semester). A two-page proposal of the group's chosen topic is due by Thursday, October 9, 2008. A two-page progress report of the group's chosen project is due by Tuesday, November 18, 2008. The term-project is due on Tuesday, December 2, 2008.

    Exams:

    Quiz: Thursday, September 4, 2008. Biology Terms.
    Midterm Exam: Thursday, October 23, 2008.
    Final Exam: Tuesday, December 16, 2008 from 9:45 to 12:00.

    The Midterm is one hour and 15 minutes long, and all exams are in-class, closed-book and comprehensive.

    The Quiz is 20 minutes long and will be given in the beginning of the lecture.
    The Midterm is one hour and 15 minutes long, and all exams are in-class, closed-book and comprehensive. You will get back your exam one week later.

    Class Attendance

    Grading Policy

    The final grade will be computed as shown below:

    Assignments 20%
    Term-project 20%
    In-class Presentation 5%
    Quiz 10%
    Midterm Exam 20%
    Final Exam 25%

    [97, 100] A+
    [90, 97) A
    [87, 90) A-
    [85, 87) B+
    [80, 85) B
    [77, 80) B-
    [75, 77) C+
    [70, 75) C
    [65, 70) C-
    [56, 65) D+
    [53, 56) D
    [50, 53) D-
    [0, 50) F

    Add/Drop Policy

    For those wishing to add this course, the deadline is September 12, 2008. The last day to drop with a full refund is September 5, 2008. According to University and Department guidelines, dropping after September 5 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.)