CS427/640/740

Bioinformatics I

Department of Computer and Information Sciences

Tuesday - Thursday

3 semester hours credit

11:00 A.M. - 12:15 P.M.

Fall Semester 2007

 

Instructor: Dr. Aubrey Hill, Ph.D.

Email: ahill@uab.edu

Phone Number: 934-0810

Office Hours: 11am to 12pm; Wednesday and Friday MEB 240 (by appointment)

 

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: Monday and Friday 8:00am to 10:00am

Location: CIS Undergraduate Computer Lab CH154

 

Textbook: Bioinformatics for Dummies by Claverie and Notredame. Wiley Publishing. ISBN 0-470-08985-7

 

Required Reading:  DNA: The Secret of Life  by James D. Watson.  Alfred A. Knopf.  ISBN 0-965-73969-4.

 

References:

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

 

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

 

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. 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.  This course will emphasize the use of bioinformatics tools as well as the underlying algorithms, but it is not a programming course.  Programming to implement bioinformatic algorithms is covered in the the second course, CS641.  Most homework assignments will involve the use of bioinformatics tools that are available on various web sites.  Students are required to keep a notebook of homework results to be handed in on each test date.  For the Fall of 2007 we will be reading, DNA: The Secret of Life by James Watson, to gain a broader knowledge of genetics and the history of the field.  A short, written summary of each chapter is to be included in the homework notebook.

 

Grading Policy

 

CS427

CS640

CS740

Homework

40%

40%

40%

Tests (3)

45%

45%

45%

Comprehensive Final Exam

15%

15%

15%

 

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 UAB 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 see: http://www.uab.edu/blazerid. All email communications will be made using this address.  e-mail is often the best way to contact the instructor.

Lectures

 

Course Schedule

1

August 23

Introduction, NCBI

2

August 28

NCBI

3

August 30

Chemistry

4

September 4

Biology

5

September 6

Metabolism/Enzymes/Proteins

6

September  11

No Class

7

September  13

Discovery of DNA as Genetic Material

8

September  18

Genetic Code

9

September  20

Lab Techniques

10

September  25

Lab Techniques

11

September  27

Finding Genes in DNA

12

October 2

Retrieving Sequences

13

October 4

Test  (Notebooks due)

14

October 9

Sequence Similarity

15

October 11

Sequence Similarity

16

October 16

Sequence Similarity

17

October 18

Scoring and Substitution

18

October 23

Multiple Sequence Alignment

19

October 25

Phylogenetics

20

October 30

Searching Sequence Databases

21

November 1

Searching Sequence Databases

22

November 6

Test (Notebooks due)

23

November 8

RNA

24

November 13

Proteins & Proteomics

25

November 15

Human Genome Project

26

November 20

Bioinformatics Resources – Web Sites & Databases

27

November 22

Thanksgiving – No class

28

November 27

Microarrays

29

November 29

Microarray Data Analysis

31

December 4

Test (Notebooks due)

 

December 13

Exam (10:45 a.m. - 1:15 p.m.  -  Notebooks due )

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

                              

 

 

 

 

Last Updated: August 21, 2007

 

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