Syllabus - BIOS 599 - Bioinformatics for Biologists - Spring 2004

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

TA: Mitch Day
Office: 604 Garrison Hall
Office Hours: By Appointment
Phone: (208)223-7788
Email: daymitc@isu.edu

Class meets:
Tuesdays & Thursdays, 9:30-10:45am in LC 4.

Overview
Bioinformatics for Biologists 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 (“How do I use Unix?”), development (“Who makes these tools? How did they do it?”), and evaluation (“How do I know which one works best for what I want to do?”).
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 (e.g., iNquiry and Vector NTI).
A survey of genome-related databases, with an emphasis of understanding how the data are generated & formatted and what their potential uses are.
Hands on experience – using bioinformatics tools to mine data.

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

Greg Gibson & Spencer V. Muse, A primer of genome science, Sinauer & Associates, 2002, ISBN: 0-87893-234-8 (about $50)

Optional:
David W. Mount, Bioinformatics: sequence & genome analysis, Cold Spring Harbor Laboratory Press, 2001, ISBN: 0-87969-608-7 (about $75)
This book provides much more depth on the algorithms underlying most common bioinformatics tools

Cynthia Gibas & Per Jambeck, Developing Bioinformatics Computer Skills, O’Reilly & Associates, 2001, ISBN: 1-56592-664-1 (about $35)
This book will help biologists develop a structured approach to biological data and the computer tools they'll need to analyze it. The book covers the Unix file system, building tools and databases for bioinformatics, computational approaches to biological problems, an introduction to Perl for bioinformatics, data mining, data visualization, and tips for tailoring data analysis software to individual research needs.

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

Project – presentation 30%
Project – written contribution 30%
Assignment - program and presentation 20%
Participation, critiques, intangibles 20%

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

Project: The Handbook of Bioinformatics for Biologists:
The project for this semester involves the creation of a “Handbook of Bioinformatics for Biologists”. This will be a web-published reference for biologists using the iNquiry suite of bioinformatics tools. Each BIOS 599 student will produce a chapter on the use of a group of related bioinformatics tools. Students will receive primary authorship credit for their summary chapter and editorial credit for the Handbook.

Project assignments:
Each student will be assigned one group of related bioinformatics tools. These assignments will be determined the first week of class – see tentative schedule for tools that will be covered. For their assigned group of bioinformatics tools, students will:

Prepare a presentation about the use of those tools in biological research. The presentation topic and date will be assigned the first week of class. 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.
Prepare a 3-5 page summary for those tools, including information about what the tools do, how the tools work, tool applications of interest to biologists, and a list of primary references (from peer reviewed publications) related to those tools and references to research applications of those tools by biologists.

Written summaries are due at the beginning of the class period in which the student presents the assigned bioinformatics tools. Students are encouraged to consult with the instructor and other students & faculty to improve their project assignment product; however, the final product will reflect work done by the student. Summary authors are expected to use the critiques (see below) to improve the quality of their summaries; therefore, the primary author will have one week to integrate comments from the various critiques. The final draft will be due two weeks after the presentation. Primary project assignments will be worth 60% of the final grade for each student: 1/2 of this based on the presentation, 1/2 on the written summary.

Project critiques, participation, and intangibles: A small portion of your grade will consist of items not easily measured and categorized. These include elements like class participation, meetings with the instructor, keeping up with the readings, using the course message boards & mailing lists, etc. Also included in this category are project critiques.

Each student will critique the project summaries prepared by the other students in the class. Critiques involve writing comments that improve the summary and help create a consistently high quality Handbook. Critique comments can include: editorial suggestions, additional relevant citations, additional tool applications, and other comments.

Critiques for each tool presentation summary will be conducted online during the week after the corresponding presentation and will be submitted via the course web server (egg.isu.edu). Instructions for posting critiques will be covered in class. The author will use the critiques to improve the written summary before the final draft is handed in (see above).

Grades for project critiques will be assigned based on the quality and quantity of the comments & suggestions made during the semester. Critiques, in addition to in-class participation and intangibles, are worth 20% of the final grade.

Assignment:
A small computer programming task will be assigned to each person. These will allow students to practice exercising their creative problem-solving skills using the computational tools covered early in the semester. The tasks will be assigned early in the semester (tentatively scheduled for January 29, 2004), and students will present your solution in a very short (5-10min), informal presentation 3 weeks later (tentatively scheduled for February 19, 2004). Students are expected to take full advantage of the talents of the instructor and the TA to ensure success. The assignment will be worth 20% of the final grade.

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