CIS 455: Bioinformatics (Fall 2005)

Instructor

Li Shen
Office: Dion 307A
Phone: (508) 910-6691
Email: lshen@umassd.edu
Office Hours: Tue 3:30-5pm, Thu 3:30-5pm, Fri 12-1pm (or by appointment)

TA

Sai Krishna Ravindran
Office: Dion 311
Email: g_sravindran@umassd.edu
Office Hours: Thu 3:30-4:30pm

Lectures

Tue and Thu, 2-3:15pm, Dion 101

Prerequisites

CIS 360 Algorithms and data structures

Course Objectives

• To study fundamentals of algorithmic principles driving advances in bioinformatics
• To study selected algorithms for solving biologically relevant problems
• To provide students with experience to link algorithmic ideas to biological topics

Course Description

This course introduces biological and algorithmic ideas together and link issues in computer science to biology. It is organized according to the following algorithmic principles.
• Exhaustive Search
• Greedy Algorithms
• Dynamic Programming Algorithms
• Divide-and-Conquer Algorithms
• Graph Algorithms
• Clustering and Trees
These algorithms are introduced and discussed for solving the following biological problems.
• Mapping DNA
• Sequencing DNA
• Comparing Sequences
• Predicting Genes
• Finding Signals
• Identifying Proteins
• DNA Arrays
• Genome Rearrangements
• Molecular Evolution

Course Materials

• Textbook
  • Neil C. Jones and Pavel A. Pevzner, An Introduction to Bioinformatics Algorithms, The MIT Press, 2004, ISBN 0-262-10106-8, http://www.bioalgorithms.info/
• Important Web Links
  • Course Homepage: http://www.cis.umassd.edu/~lshen/courses/2005_fall_cis455/index.htm
  • Textbook Homepage: http://www.bioalgorithms.info/
• Recommended References
  • Introduction to Matlab: http://www.cs.dartmouth.edu/~farid/tutorials/matlab.intro.html
  • Matlab online documentation: http://www.mathworks.com/access/helpdesk/help/helpdesk.html
  • Matlab Primer: http://ise.stanford.edu/Matlab/matlab-primer.pdf

Homework

• Homework assignments will be posted online. Homework is due at the beginning of class on the announced due date. Any exceptions must be approved by the instructor in advance. Late homework will not be accepted.
• Some of the exercises will be routine, but others will be more challenging. I hope that you will benefit from working on the more difficult ones.
• I encourage discussion of homework assignments between students. However, your submitted homework must be entirely your own. You may not copy anything directly from another student's work. You should note with whom you discussed the problem at the beginning of your solution write-up. Note that discussion between two students will be most useful when both students have already made serious attempts to solve the problem on their own.

Requirements and Grading

There will be homework assignments, a class presentation, a term project, a midterm exam, and a final exam. Class attendance is mandatory. You are responsible for all announcements and for all material presented in the lecture sessions. Come prepared for class and read the assigned material in advance of lectures. After the lecture, re-read the material. The evaluation will be based on:

• Homework: 30%
• Presentation: 10%
• Term project: 10%
• Midterm exam: 20%
• Final exam: 25%
• Class participation: 5%

The letter grades will be assigned using the following approximate scale: (A+,A,A-)[100-90], (B+, B, B-)[90-80], (C+,C,C-)[80-70], (D+,D,D-)[70-60], and F[60-0].

Important Dates

• 10/25/05: Midterm exam
• 11/03/05: Project proposal due
• 12/15/05: Project due
• 12/21/05: Final exam

Academic Honesty

• The UMass Dartmouth Academic Ethical Standards and Student Judicial Code apply to your conduct in this course. Please refer to the following materials for details.
  • Student Handbook (http://www.umassd.edu/studenthandbook/)
  • Academic Ethical Standards (http://www.umassd.edu/studenthandbook/academicregs/ethicalstandards.cfm)
  • Student Judicial Code (http://www.umassd.edu/studenthandbook/studentjud/)
• All work submitted for credit must be your own. You may, however, discuss your homework assignments and term project with your classmates and Professor Shen.
  • For written homeworks, you should writeup your own solutions and neither read nor copy another person's solution or portions of their solution - this includes solutions from any web page (other than our class web page) that you find on the web.
  • For programs, you should create and type in your own code, and any copying (electronic or otherwise) of another person's code or code fragments is a violation of the Academic Ethical Standards.
  • You cannot collaborate or copy in any way on exams.
• If you have any questions as to whether some action would be acceptable under the Academic Ethical Standards, please speak to me, and I will be glad to help clarify things. It is always easier to ask beforehand than to have trouble later!

Disability Statement

If you have a disability and feel you will need accommodation in order to complete course requirements, please contact Office of Disabled Student Services, Group I, Lower Level.