BME 060 - Spring 2004

Programming for Biologists and Biochemists

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Course Information

Lecture: Tu 10-11:45am, Baskin 372 Lab: Th 10-11:45am, Porter D-245 Arts DML Computer Lab

Information and Handouts

· Office Hours

· Syllabus & Lecture slides

· Labs & Problem Sets

· Frequently Asked Questions

Course Description & Objectives

Teach programming skills to students who are preparing for careers in biology and the life sciences.

The course will be laboratory oriented to give hands-on experience with most of the basic and several intermediate programming constructs. In addition, they will become advanced users of biology-specific programming libraries that are maintained and provided as open source by the bioinformatics community. Some examples of what the students will have first hand experience in include:

· Computing statistics on biological sequences.

· Writing pattern discovery methods

· Manipulating a wide range of data formats

· Communicating with remote biological databases

· Calling and parsing output retrieved from local and remote servers

Prerequisites

There are no pre-requisites required for this course. It is designed to teach students how to write and run their own programs using the Perl programming language.

Polices

Grading

Grades are based 80% on 4 programming assignments, 20% on a project proposal.

Credit will be given for class presentation.

Late policy. Each person has 7 late days to use however they see fit. When you turn in your homework, please note the number of late days you are using.

Working in Groups

Encouraged to work together on program assignments in groups of no more than 3. Please list the names of your teammates on what you turn in.

If any of you have programming experience, please try to team up with those who do not.

Communication

We strongly encourage students to come to office hours.

Please do not e-mail the instructors with grading questions. If you want us to explain why we took points off, you can talk to us after class or during office hours. If you want a re-grade, please write an explanation and hand the homework and the explanation to one of the instructors during office hours or after class.

Occasionally we may need to broadcast a message to entire class. To make sure we can reach you, please subscribe to the BME60 mailing list by sending an e-mail to majordomo@lists.ucsc.edu with a blank subject line and "subscribe bme60" as your message.

Textbook Information

· The required reading material will be the book “Beginning Perl for Bioinformatics” by James Tisdall.

· An optional text more advanced topics is the book “Mastering Perl for Bioinformatics” also by James Tisdall.

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