CS427/640/740

Bioinformatics I

Department of Computer and Information Sciences

Tuesday

3 semester hours credit

5:30 P.M. - 8:00 P.M.

Fall Semester 2009

 

Instructor: Dr. Aubrey Hill, Ph.D.

Email: ahill@uab.edu

Phone Number: 934-0810

Office Hours:  After Class, Campbell Hall 140 (by appointment)

 

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

 

Prerequisites: Graduate standing, approved background in a biological science and permission of instructor.

Classroom: CH430

 

Teaching Assistant:

Office Hours:

Location:

 

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 2009 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. Graduate students will be required to do a short paper on a topic to be assigned.

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 18

Introduction, NCBI

2

August 18

NCBI

3

August 25

Chemistry

4

August 25

Biology

5

September 1

Biology

6

September 1

Metabolism/Enzymes/Proteins

7

September 8

Discovery of DNA as Genetic Material

8

September 8

Genetic Code

9

September 8

Lab Techniques

10

September 15

Lab Techniques

11

September 15

Finding Genes in DNA

12

September 22

Retrieving Sequences

13

September 22

Test (Notebooks due)

14

September 29

Sequence Similarity

15

September 29

Sequence Similarity

16

October 6

Sequence Similarity

17

October 6

Scoring and Substitution

18

October 13

Multiple Sequence Alignment

19

October 13

Phylogenetics

20

October 27

Searching Sequence Databases

21

October 27

Searching Sequence Databases

22

November 3

Test (Notebooks & Graduate papers due)

23

November 3

RNA

24

November 10

Proteins & Proteomics

25

November 10

Human Genome Project

26

November 17

Bioinformatics Resources  Web Sites & Databases

27

November 17

Microarrays

28

November 24

Microarray Data Analysis

29

November 24

Test (Notebooks due)    

31

November 29

Thanksgiving  No class

 

December 1

SNPs, HapMap, dbSNP, 1000 Genomes Project

 

December 8

Exam (Notebooks due )

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 



Last Updated: July 21, 2009

 

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