CS427/640/740

Bioinformatics I

Department of Computer and Information Sciences

Tuesday - Thursday

3 semester hours credit

11:00 A.M. - 12:30 P.M.

Fall Semester 2006

 

Instructor: Dr. Aubrey Hill, Ph.D.

Email: ahill@uab.edu

Phone Number: 934-0810

Office Hours: 11am to 12pm; Wednesday and Friday MEB 240

 

Course Homepage: http://www.cis.uab.edu/cs640

 

Prerequisites: Graduate standing, approved background in a biological science and permission of course coordinator

Classroom: CH430

 

Teaching Assistant: Vetria Byrd (vlbyrd@uab.edu)

Office Hours: Tuesday and Thursday 8:00am to 10:00am

Location: CIS Undergraduate Computer Lab CH154

 

Textbook: Bioinformatics Sequence and Genome Analysis 2nd Edition by David W. Mount. Publisher: Cold Spring Harbor Laboratory Press, 2004. ISBN: 0-87969-712-1.

 

References:

Genes VII or GenesVIII by Benjamin Lewin. Publisher Oxford University Press. ISBN 0-19-879276-X

 

Bioinformatics for Dummies by Claverie and Notredame. Publisher Wiley Publishing. ISBN 0-7645-1696-5

 

Medical Genetics by Jorde, Carey Bamshad and White. Mosby Publishing. ISBN 0-8151-4608-6

 

Computational Methods in Molecular Biology by Salzber, Searls, and Kasif. Publisher Elsevier. ISBN 0-444-50502-1

 

Course Description

This course is the first of a two-course sequence CS640/CS641 that is designed to provide an introduction to selected topics in bioinformatics with particular focus on computational challenges that are important to the UAB research community.

 

Grading Policy

 

CS427

CS640

CS740

Tests (3)

75%

75%

75%

Final Exam

25%

25%

25%

 

Class Conduct
  1. Students are expected to conduct themselves in a professional manner.
  2. Laptops will be allowed only for the purpose of the class.
  3. Students must turn their cell phones/pagers OFF during the class.

 

Class Attendance
  1. Attendance is mandatory for this course. If you know you will be absent for a legitimate reason, let the instructor know. If you are sick bring a doctor's excuse or a written university excuse to resolve the absences. An absence has to be resolved as soon as possible - otherwise it will not be treated as an excused absence.
  2. Students auditing this course are expected to attend the lectures. Auditing students with more than three unexcused absences will receive a failing grade.
  3. There will be NO make-ups for tests. A student anticipating an excused absence from a test should make arrangements in advance to sit for the exam at another time.

 

Academic Honesty

Students who plagiarize a computer program (or parts of a program), get others to write a program (or parts of a program), or are found cheating on a quiz/exam, will be reported for academic dishonesty. Anyone who is caught cheating will receive a 0 on a given test or assignment. If a second offense occurs, the student will receive an F in the class. This includes both the provider of the information as well as the receiver of the information. Any student who violates the university's academic honesty policy will be reported for academic discipline. All university and department policies related to students are included here by implication.

 

E-mail

Every student will be required to use his/her official email address that is blazerid@uab.edu. New students must login and configure their email addresses. For more details on obtaining blazerID and configuring email please see: http://www.uab.edu/blazerid. All email communications will be made using this address. Additional instructions or announcements will be sent by e-mail, so check your mail often - at least twice a day (once in the morning and once at night). Also check the course webpage for up-to-date information and announcements. Instructor will check email frequently, so e-mail is often the best way to contact the instructor.

 

Course Schedule

1

August 22

Introduction

2

August 24

Biochemistry

3

August 29

Biology

4

August 31

Metabolism/Enzymes/Proteins

5

September 5

DNA as genes

6

September 7

DNA as genes

7

September 12

What biologists want (Vetria Byrd)

8

September 14

RNA

9

September 19

Genomics

10

September 21

Proteomics

11

September 26

Lab Techniques

12

September 28

Test 1

13

October 3

Microarrays

14

October 5

Bioinformatics Tasks

15

October 10

Pairwise alignments

16

October 12

Dot matrix/dynamic programming

17

October 17

Needleman/Wunsch

18

October 19

Smith-Waterman

19

October 24

Significance

20

October 26

FASTA

21

October 31

BLAST

22

November 2

Test 2

23

November 7

Multiple alignments

24

November 10

Gene finding

25

November 14

Phylogeny

26

November 16

Protein classification/structure prediction

27

November 21

Thanksgiving No class

28

November 23

Prediction of RNA secondary structure

29

November 28

Microarray Data Analysis

30

November 30

Bioinformatics web sites & databases

31

December 5

Test 3

 

December 14

Comprehensive Final Exam 10:45am to 1:15pm

 

Last Updated: August 29, 2006

 

Dept. of Computer and Information Sciences * The University of Alabama at Birmingham

115A Campbell Hall, 1300 University Boulevard * Birmingham, Alabama 35294-1170

Phone: 205.934.2213 * Fax: 205.934.5473