PROGRAMMING FOR BIOLOGY
October 15 - 28, 2008
Application Deadline: July 15, 2008

Instructors:
Suzanna Lewis, University of California, Berkeley
Simon Prochnik, University of California, Berkeley
James Tisdall, Dupont Corporation & Biocomputing Associates

A computer is already an indispensible tool for database searches, but the use of web-based tools alone is not enough for today’s biologist who needs to acess and work with data from myriad sources in disparate formats. This need will become ever more important as new technologies increase the already exponential rate at which biological data is generated. Designed for students and researchers with little or no prior programming experience, the two-week Programming for Biology course will give biologists the bioinformatics skills necessary to exploit this abundance of biological data.

The course is based around the Perl scripting language, because of its ease of learning and its incredible wealth of ready-built code modules (e.g. bioperl) designed to solve common biological problems. Starting with introductory coding, and continuing with a survey of available biological libraries and practical topics in bioinformatics, students end by learning how to construct and run powerful and extensible analysis pipelines in a straightforward manner. The course combines formal lectures with hands-on sessions in which students work to solve problem sets covering common scenarios in the acquisition, validation, integration, analysis and visualization of biological data. For their final projects, which run during the second week of the course, students will pose problems using their own data and work with each other and the faculty to solve them. Final projects have formed the basis of publications as well as public biological websites (see, for example: http://bio.perl.org/wiki/Deobfuscator).

The prerequisites for the course are basic knowledge of UNIX. Lectures and problem sets covering this background material are available online from previous years and students can study this material before starting the course. Note that the primary focus of this course is to provide students with practical programming experience, rather than to present a detailed description of the algorithms used in computational biology. For the latter, we recommend the Computational Genomics course.

Speakers in the 2007 course included: Tyler Alioto, Emina Begovic, Scott John Cain, George Hartzell, Matt Hibbs, Gabor Marth, Jason Stajich, Paul Thomas & Mark Yandell.

This course is supported by the National Human Genome Research Institute