ELEC 498/898
Introduction to Bioinformatics

TR, 2:00 - 3:15, W185 NH
Fall 2005

Instructor: Khalid Sayood (472-6688)
Office Hours: 235N WSEC, 3:30- 4:30 TR These office hours are not exclusive. You are welcome to stop and talk with me any other time you find me in my office. You can also reach me via email.
Credits: 3 credit hours
Text: Computational Molecular Biology: An Introduction P. Clote and R. Backofen, Wiley. I will attempt to supplement this with handouts.

The net has a wealth of resources devoted to bioinformatics. Click here for some links.

Announcements:

Goal:

Bioinformatics is a relatively new and rapidly growing area. In fact the rapidity of its growth makes it difficult to provide a precise definition of bioinformatics. I see bioinformatics as a study of how information is organized in the genome and I tend to approach the study of bioinformatics from this perspective. However, regardless of your particular perception or bias there are certain basic ideas and concepts that are common to most definitions of bioinformatics. The goal of this course is to provide a base from which you can explore the aspects of bioinformatics that most interest you. A tentative list of the topics to be covered include:

Overview of chemical basics.
Overview of biological aspects of DNA.
Sequence alignment and sequence databases.
Molecular phylogeny.
Regulation and regulatory networks.
Microarrays

The amount of time we spend on each topic will not be the same and, based on your interest we will add further topics to this list.

Assignments:

There will be assignments of three different types:

Reading Assignments: This will involve reading papers from the technical literature and preparing critiques.
Chapter Problems: These will be assignments of the standard variety - problems from the end of the chapter.
Programming assignments: These will require making use of popularly used bioinformatic tools and implementations of the techniques we will be studying. They will make up the majority of the assignments. As most bioinformatics tools are available for the UNIX enviroment make sure you have access to a UNIX platform. (If you do not have access to a UNIX platform please let me know.) You should be reasonably comfortable in this environment. If you are not you can use any of number of tutorials on the web (like this one, or this one) to get a working knowledge.

You will also be doing a final project in lieu of the final exam. This will be a project of your choosing. Multiple person proposals are acceptable with a commensurate increase in the scope. Project presentations will be scheduled for the last week of classes.

Grading:

Homework	40%
Two hour exams	30%
Final project	20%

Cheating:

Most of you are honest individuals. If you feel the temptation to cheat, resist it. If you cheat, even if you don't get caught, you will have compromised your integrity which is probably your most valuable possesion. If you do get caught, the consequences include an F in the class and possible disciplinary proceedings. If you help someone to cheat you may also face the same consequences.

A complication with programming assignments is that you will end up using resources in ways that you feel are totally justified which may look different from my perspective. In order to avoid any misunderstandings I want you to attach a "resources used" sheet to each programming project. This should include all resources (animate and inanimate) that you used in the course of completing this project. It is in your interest to provide as complete a list as possible.

Comments/Questions?