James A. Foster

Home Up Next

Perl for Bioinformatics

ST: CS 4/504-01 (1 cr)

James A. Foster (foster@cs.uidaho.edu)

Announcement: Be sure to check the materials webpage! Also, there is a notes page, which lecture notes and other stuff.

And here is the syllabus. 


bullet I will not be in class on 18 January, but you should be. Please take attendance at this first meeting. Everyone, sign in on a sheet of paper including your name and email ID. To prepare for class, you should read the first 3 chapters of the text, and be sure you have access to Perl. One easy way to do that is to install Perl on your own machine. The book says how to do this. In class, please discuss any problems you had installing Perl.
bullet To prepare for the 24 Jan class, please read chapter 4 of the text and work as many of the exercises as you can. We will go over the exercises in class on 24 Jan.

Place and Time 15.30-16.20, Thurs. BEL 205.


Bioinformatics uses computation and mathematics to interpret biological data, such as DNA or protein sequences or structures. An important practical skill in this field is the ability to develop quick and dirty scripts (short programs) for scanning or transforming large amounts of data. The programming language of choice for this is Perl, due to its compact syntax, data orientation, and built in pattern matching facilities.

In this course, we will work our way through the textbook, implementing several Perl scripts along the way. We will discuss our solutions in class. Along the way, we will learn some of the basic types of problems that bioinformaticians explore. But the main benefit of the course will be a practical understanding of how to design and implement Perl scripts for bioinformatics problems.

The objective of this course is to improve interdisciplinary research in bioinformatics and to advance our ability to transform biological data into biological knowledge.  This is part of the mission of the Initiative for Bioinformatics and Evolutionary STudies (IBEST), (see www.cs.uidaho.edu/ibest). For more information, please contact Dr. Foster (foster@cs.uidaho.edu).

Course Details

This is a one credit class, so you should expect to spend about 3-4
hours a week on it. It may take more time at first if you don't have
much programming experience. We will meet weekly to discuss the readings and exercises that we worked on during the previous week. Each week we will read the next chapter in the text, and do as many exercises as we can. Each week I would like you to turn in copies of your exercise answers to me. Your grade will be determined by effort and class participation (class attendance is mandatory and will count toward the grade).

Please note that this is not a lecture class, it's a discussion class.
More of a workshop, really. So come prepared to discuss.

We do NOT currently have access to a computer in our classroom. So, if
you can bring laptops to class that would help. If you can't (or don't
have one), don't worry. Just be prepared to talk about programming
without having access to a computer (a sub-optimal solution, but we do
what we can, eh?)

Computer Science Home Page Univ. of Idaho Home Page

Last Updated 01/13/2003 15:56 -0800