BME 060 & BME 160 - Winter 2006 Programming for Biologists and Biochemists

Course Information

Lecture Location: Earth & Marine Sciences, Room B210
Lecture Time: Tu/Thu 12-1:45am
Lab Location: Soc Sci I Mac Lab (Room 135) [Map to lab]
Lab Time: Wed 12-1:45am

Information and Handouts

• Instructor Info & Office Hours
• Syllabus & Lecture slides
• Lab Assignments
• Lab Notes
• 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 computer-related 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.

Research Projects

Students enrolled in the upper-division level of the course are expected to complete a final research project. The research project should be chosen in consultation with the faculty instructor(s). Research projects should investigate a question related to research in the biological sciences and should make use of significant programming skills as part of the aims of the project.

Polices

Grading

Grades are based on 6 programming assignments (tentative), 8 quizzes, and the final research project (for those taking the upper division level of the course). Credit will be given for class participation.

Late policy
Each person has 7 late days to use. For any assignment, only a total of 3 late days may be used. When you turn in your homework, please note the number of late days you are using. After all 7 of your late days are used, a penalty of 10% will be applied for each late day.

Working in Groups

You are 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 or contact either the instructor or TA via e-mail. We check our e-mail regularly and you should receive a timely response.

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, we will be using a class mailing list. The class e-mail list is bme60@ucsc.edu. Instructions on how to subscribe will be provided within the first assignment.

Textbook Information

	The required reading material will be the book “Beginning Perl for Bioinformatics” by James Tisdall. The bookstore prices are $39.95 for new and $30 for used. Cheaper prices can be found on the web.
	An optional text for convenient reference is “Perl Pocket Reference” by Johan Vromans. The  4th edition is the latest.  The 1st edition while out of date is freely available here in pdf format or html. The bookstore prices are $9.95 for new and $7.50 for used. Cheaper prices can be found on the web.
	UCSC has a limited Safari subscription. Safari is an online library of computer books and contains several useful Perl and UNIX references. A sample list of books that will likely be relevant to this class is shown below: Perl in a Nutshell Sequence Analysis in a Nutshell Learning Unix for Mac OS X Panther Mac OS X Panther in a Nutshell Mac OS X Pocket Guide Note: Safari is only available from the ucsc.edu domain (in other words you must either be on campus or using a proxy).

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