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Timothy Collins
Accessing and Working with Molecular Biological Databases and Internet Resources, BSC 6456C
Course Description:

The purpose of this workshop is to familiarize Biology graduate students with relevant molecular biology resources on the Internet. It will include a survey of databases and resources available, methods of searching databases, uses of programs available on the Internet, and an introduction to methods of analyzing data. The workshop assumes a basic working knowledge of desktop computers and molecular biology (at least 1 undergraduate course in genetics or molecular biology and basic familiarity with word processing and spreadsheet programs).

Instructors and Contact Information:

Tim Collins: OE 212, PH: 305-348-1730, e-mail:CollinsT@fiu.edu, Office hours: Tuesdays 9:00-12:00.
David N. Kuhn: OE 230, PH: 305-348-6576, e-mail: KuhnD@fiu.edu, Office hours: Fridays, 11:00- 1:00.

Schedule:

The class will meet in the Macintosh computer lab (PC449)on Fridays 1:00-4:00pm for seven weeks. For each section, we will have an introductory lecture and/or demonstration followed by a tutorial on the topic of the week.

Date Topic Reading
09/17 Organizational meeting Chapters 1 & 2
09/24 Introduction to Internet resources for Molecular Biological Research (Collins) Chapters 3, 5 & 7
10/01 Homology, Similarity, Multigene Families, and Alignment (Collins) Chapters 8 &9
10/08 Phylogenetic Analysis with Molecular Data (Collins) Baldauf, 2003
10/15

Structure and Function of Genes and Proteins

(Kuhn)

Chapters 10 &11
10/22

Introduction to GCG package for DNA and Protein sequence analysis

(Kuhn)

Chapter 14
10/28

Motif Searching of Databases [SeqLab tutorial]

(Kuhn)

 

Grades will be based on the performance on weekly tutorials. Tutorials will include questions that must be answered and turned in. Answers are due by the beginning of the next class. Write answers in the spaces provided on lab, and turn them in. Labs will be returned the following week. You may discuss these exercises with your classmates. These are not, however, group efforts. Tutorials that are essentially duplicates of one another are unacceptable and will result in a failing grade for both parties.

Please put your name on all materials turned in with labs, and staple or paper clip pages. We will accept labs for grading up to one week late, although they will be marked down for lateness. Labs that are more than one week late will not be graded.

Textbook: Baxevanis A. D. and Ouellette, B. F. F. 2001. Bioinformatics: a practical guide to the analysis of genes 2nd Edition. Wiley.