PROGRAMMING FOR BIOLOGY
October 18 - 31, 2006
Application Deadline: July 15, 2006

Instructors:
Suzanna Lewis, University of California, Berkeley
Simon Prochnik, University of California, Berkeley
Lincoln Stein, Cold Spring Harbor Laboratory
James Tisdall, Dupont Corporation & Biocomputing Associates

Today, the computer is an indispensable part of a research biologist's toolkit. The success of the human and other organism genome projects has created terabytes of data on everything from genetic linkage mapping, to nucleotide sequences, to protein structures, stashed away in databases around the globe. Large-scale technologies such as DNA microarrays and high-throughput genotyping have transformed the nature of laboratory experimentation. Furthermore, even when biologists are not generating large data sets of their own, they will want to collect and analyze data from myriad sources in the pursuit of novel candidates or even entire research avenues. A few years ago it might have been sufficient to use Excel spreadsheets for managing laboratory data and canned Web interfaces for searching, but as the volume of data grows and the subtlety of analysis increases, these techniques, even supplemented by some simple programming skills, have become inadequate. Modern biologists must be adept at juggling disparate data sets in order to pursue their research. Designed for students and researchers with some prior programming experience, the two-week Advanced Bioinformatics program will give biologists the expanded bioinformatics skills necessary to construct computational systems that can exploit this increasingly complex information landscape, with an emphasis on fitting the wide range of existing analysis tools into extensible bioinformatics systems. The course combines formal lectures with hands-on sessions in which students work to solve a series of problem sets covering common scenarios in the acquisition, validation, integration, analysis and visualization of biological data. For their final projects, students will pose problems using their own data and work with each other and the faculty to solve them. The prerequisites for the course are basic knowledge of UNIX, procedural Perl programming, HTML document creation and the database query language, SQL. Lectures and problem sets covering this background material are available online 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 2005 course included:
Emina Begovic, University of California, Berkeley
Peter Brokstein, DOE Joint Genome Institute
Roderic Guigo, Institut Municipal d'Investigacio Medica, Spain
Winston Hide, University Western Cape, South Africa
Gabor Marth, Boston College
Sheldon McKay, Cold Spring Harbor Laboratory
Chris Mungall, Berkeley Drosophila Genome Project
Lior Pachter, University of California, Berkeley
William Pearson, University of Virginia
Jason Stajich, Duke University
Paul Thomas, Applied Biosystems
Olga Troyanskay, Princeton University

This course is supported by the National Human Genome Research Institute