Syllabus for BIOS 599

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Instructor: Michael A. Thomas, Ph.D.
Office: 256 Gale Life Science
Office Hours: 11am – 12pm Tuesday & 10am - 12pm Wednesday
Phone: (208) 282-2396
Email: mthomas@isu.edu

Class meets:
Tuesdays & Thursdays, 9:30-10:45am in LC 4 or Gale 208 (the bioinformatics Mac lab).

Overview
Practical Bioinformatics is an introduction to theory and methods used for genome-level sequence analysis. The course is designed to provide biologist a set of tools and the perspective & skills to use them. The goal is for the student, at the end of the semester, to be able to have new insights into their own research. This will be accomplished through:

An overview of the fundamentals of bioinformatics, with an emphasis on usage, integration, and interpretation. This will be accomplished through lectures, discussions, and readings.
A survey of bioinformatics tools, with an emphasis on tools for comparative genomics, including major stand-alone tools (e.g., BLAST and HMMer) and suites of tools. This will be accomplished through weekly in-class computer exercises and assignments.
The in-depth exploration of a set of tools to address a specific biological problem. This will be accomplished as a project chosen by each student (see below).

Course information and computational resources can be accessed at http://egg.isu.edu

Topics covered:
Please see attached schedule. Coverage and dates are subject to change.

Prerequisites
A background in molecular genetics and experience with the Unix computing environment will be helpful but not essential.

Textbook & References
Required (available at the bookstore):
David W. Mount, Bioinformatics: Sequence and genome analysis, second edition, Cold Spring Harbor Lab Press, 2004, ISBN: 0-87969-712-1 (about $90)

Optional reference guide (available at the bookstore):
Scott Markel & Darryl León, Sequence analysis in a nutshell, O’Reilly & Associates, 2003, ISBN: 0-596-00494-X (about $30)

Grading:
Your grade will consist of the following components, weighted as shown:

Assignments (5): 65%
Project: 30%
Participation, intangibles: 5%

Final letter grades depend upon the overall performance and may be adjusted upward.

Assignments:
Each week, generally on Thursdays, we'll work together on computer-based bioinformatics exercises to gain practical experience about the tools and approaches that we discussed the previous class. Five of these exercises will be written up as an assignment. Each assignment will involve writing 2-3 paragraphs interpreting the results of the data analysis. Most of the data analysis will be performed as a group in class, so it's important to concentrate on interpretation and synthesis for the assignment. Assignments will be due in class one week following the class in which they were assigned.

Project assignments:
Each student will choose a biological, data-intensive problem related to their own area of research. Using these data, the student will formulate a bioinformatics approach to data analysis and select the appropriate tools to do the work. Examples of previous projects may be found on last year's Bioinformatics course website. Student are encouraged to discuss their chosen project with the instructor before beginning work; topics must be chosen before spring break. For their assigned group of bioinformatics tools, students will:

Prepare a presentation about the bioinformatics approach to solving the specific problem. Presentations will be given the last week of classes. Students are expected to provide an overview about what the tools do, how the tools work, and tool applications of interest to biologists with an emphasis on applications that allow new and unique insights into the chosen problem.
Prepare a 1-2 page summary of the project. Students are expected to provide a small amount of background information about the problem, outline their approach, discuss the bioinformatics tools and approaches, interpret the results of the analysis, and a list appropriate primary references (from peer reviewed publications) related to those tools and references to research applications of those tools by biologists.

Late policy:
Assigned work in this course must be turned in by the specified due date. Late work will not be accepted.