BME 60/160 - Winter 2008 Programming for Biologists and Biochemists

Course Information

NOTE: The first class -- Wednesday, Jan 9, will meet in the Social Sciences I Mac Lab. Look on the Instructional Computing map to see where the lab is located. Following these dates, lectures will be held on Mondays and Fridays in Baskin 372 and the labs will be held on Wednesdays in the Social Sciences I Mac Lab.

Lecture Location: Baskin Engineering, Room 372
Lecture Time: Mondays & Fridays 2-3:10pm

Lab Location: Social Sciences I Mac Lab (Social Sciences Room 135)[Map]
Lab Time: Wed 2-5:30pm

Final Exam: Tuesday, March 18 8-11 AM, Baskin Engineering 372.

Information

• Instructor Info & Office Hours
• Schedule, Lecture slides, and Lab assignments
• Frequently Asked Questions (including how to get this running on a PC).

Course Description & Objectives

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

The course is lab oriented to provide hands-on experience with basic, and some intermediate, programming constructs. In addition, students will become familiar with biology-specific programming libraries that are maintained and provided as open source by the bioinformatics community. Some examples of what the class will include are:

· 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. The first laboratory will cover introductory UNIX topics.

Policies

Grading

Grading for BME 60: Programming assignments 50%, Quizzes 30%, Final exam 20%

Grading for upper division version: Programming assignments 50%, Quizzes 20%, Final project 15%, Final exam 15%

Approximate grading scale: 85-100% A, 70-84% B, 55-69% C, 40-54% D, <40% F

Programming assignments: There will be five programming assignments, with each assignment due one to three weeks after it is assigned. Each student can use up to 7 late days without penalty, with a maximum of 3 late days for any given assignment. We will deduct 10% from the grade for every late day in excess of the allowed late days.

Quizzes: There will be a 15-20 minute quiz at the start of Wednesday labs covering the material from the previous week’s lectures and lab period. We will drop the lowest two quiz scores in calculating the final grade.

Final exam/project: All students will have a cumulative final exam on Thursday, March 18 from 8-9:30 AM in Physical Sciences 305. Students taking an upper division version of this course will complete a final project using Perl programming in a non-trivial way to investigate a biological problem. The research project should be chosen in consultation with the instructor and an outside faculty advisor. The deliverables for this project include a 5-10 page report and a 5 minute oral presentation on Wednesday, March 12 in Physical Sciences 305 after the final exam.

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.
	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: Learning Perl Mastering Regular Expressions 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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