Research Programming in the Life Sciences

Programming for Biologists and Biochemists

Course Information

Description

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 topics the class will cover are:

  • Computing statistics on biological sequences and experimental data.
  • 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.

This quarter, we will be making use of Python 3.3.  This is a departure from previous quarters and is intended to prepare students for future work. If you are intending on using your personal computing resources you will no doubt need to download Python3; available for Mac, Linux and Windows.

eCommons

Most of the assignments and course resources will be available through eMommons.  Maake sure to sign up for your gold password to access the site.

Lecture

  • Location: College 8, RM 240
  • Times: Tuesday and Thursday 12:00 -1:45p.m.

Labs

Textbook

Required: Bioinformatics Programming Using Pythonby Mitchell Model. (ISBN: 059615450X, available at Amazon.com or Kno.com)

Optional: Python Pocket Referenceby Mark Lutz

Tutorials: http://docs.python.org/3.3/tutorial/

Final Exam

Final Exam: Monday, June 10 12:00 - 3:00 p.m., College 8, RM 240

Instructor: David Bernick

  • Email: dbernick@soe.ucsc.edu
  • Office: Baskin Engineering 269A
  • Office Phone: NA

Office Hours: Tuesday / Thursday 10:00-11:30 a.m. or by email appointment

Teaching Assistant: Dorothy Oliver

  • Email: doliver@soe.ucsc.edu
  • Office: TBD
  • Office Hours: TBD

Additional Assistance

If you qualify for classroom accommodations because of a disability, please submit your Accommodation Authorization from the Disability Resource Center (DRC) to the instructor during his office hours in a timely manner, preferably within the first two weeks of the quarter. Contact DRC at 459-2089 (voice), 459-4806 (TTY).

Instructors and Assistants