[Bioperl-l] COURSE: 2013 CSHL Programming for Biology Course

Sofia Robb sofia at sofiarobb.com
Mon Jul 8 18:34:35 UTC 2013

Course announcement - Application deadline, July 15, 2013


Oct 14 - 29, 2013
Application Deadline: July 15, 2013


Simon Prochnik, DOE Joint Genome Institute
Sofia Robb, University of California Riverside

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 access 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 incredible wealth of ready-built modules such as Bioperl
that are 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 (http://gorgonzola.cshl.edu/pfb/2012/) 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 & Comparative Genomics course.

Speakers in the 2012 course included:
Scott Cain, Jer-ming Chia, Brian Haas, Winston Hide, Tomas Marques-Bonet,
Gabor Marth, William Pearson, Michael Schatz, Jason Stajich, Paul Thomas,
Jim Tisdall

To apply to the course, follow the instructions at:

Sofia Robb, Ph.D
Wessler and Stajich Laboratories
University of California Riverside

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