AS 250.265 Bioinformatics (Policies)

Bioinformatics is a rapidly growing field that integrates molecular biology, biophysics, statistics, and computer science. Fundamentally it is a field focused on comparison: how similar are two given proteins? What are the differences between various DNA sequences? How is the data from one microarray assay different from another? Furthermore, bioinformatics is concerned with quantifying the significance of these differences. In any of the examples above, once a metric for similarity is obtained, it must also be statistically characterized to determine the likelihood that such a relationship could occur by chance. In this course, you will learn many of the popular tools for performing bioinformatics analysis and you will be introduced to the thinking that drives the algorithms.

The course will meet Thursdays and Fridays from 1:00 to 2:30 PM in Jenkins 122. The general format of the course will be a lecture on Thursday and a brief lecture/lab on Friday. A specific schedule of meeting times is given below. Because of the interactive nature of both lectures and labs, attendance is mandatory for the course. Please contact the instructor if you must miss a class meeting.

The textbook for the class is Bioinformatics and Functional Genomics by Jonathan Pevsner (2003 John Wiley and Sons, Inc., ISBN 0-471-21004-8). The book is available in the bookstore, but it may be cheaper for you to purchase it online (try www.addall.com). If you have a choice, try to obtain the third printing of the book, with chapter headings in red. In addition, there will be supplemental readings throughout the semester of papers and additional handouts. It is expected that you come to class having read the material.

Throughout the course, you will have weekly problem sets to test you on the material taught. These assignments are graded and constitute 20% of your final course grade. Homework assignments will often have a computational component to them, and they may partially consist of the lab from that week. You will submit these assignments using the course web server. You are free to submit the written portions of each assignment either electronically (Word document, postscript file, or PDF) or by hand at the beginning of the class period when the assignment is due. Late assignments will not be accepted unless prior arrangements with the instructor are made. In these cases, there must be extenuating circumstances (not simply a test in another course scheduled for the same day).

The grades for the course will be calculated according to the table below. Although attendance is not explicitly included, the instructor reserves the right to deduct 5 percentage points from your final course grade if you miss more than three classes.

Course Component	Percentage
In-Class Exams (3)	60%
Homework (10)	20%
Final Project	20%

If the distribution of necessitates it, the final grades will be curved. However, if all students do well, they should not expect to receive poor grades simply because of a forced bell curve on the final distribution. Students are encouraged to concentrate on learning, which has lifelong benefits, rather than grades, which are useful to your mid-twenties at best. No student who has shown discipline in pursing educational excellence will fail this course.

The ultimate goal of this course is application. To this end, there will be a final project in lieu of a final exam. This project will be due during the final examination period, on or before 12:01 am (the morning of) Monday, May 15, 2006. You will be able to choose from a choice of final projects: one project will involve characterizing an unknown genetic sequence provided by the instructor. Another project possibility will involve identifying an as yet undiscovered gene and describing its possible function. Finally, you are welcome to design a web application implementing one of the algorithms discussed in the course. If you choose this last option, you are allowed to work with one partner. More information on the final project will be provided at a later date.

The instructor will be available for course help in his office on most Thursday mornings from 10:00 am to 12:00 pm. If you are unavailable then and wish to schedule an alternative time to meet, please send email to the instructor. Drop-in appointments are welcome, but may need to be rescheduled depending on the instructor's schedule.

Please check this site frequently for course updates. Additionally, many of the homework assignments will be distributed through this site, and you will be able to submit your assignments through this web site as well.

Download a copy of these policies here.