October 13 - 28, 2014
Application Deadline: July 15, 2014
Prochnik, DOE Joint Genome Institute
Sofia Robb, Stowers Institute for Medical Research
of Honor - who's taken the course in the past
Web-based tools are no longer enough for today's biologist who needs to access and analyze large datasets from myriad sources in desparate formats. The need to design and program custom analysis pipelines is becoming ever more important as new technologies increase the already exponential rate at which biological data is generated. Designed for lab biologists with little or no programming experience, students will leave the two-week Programming for Biology course with the bioinformatics and scripting skills necessary to exploit this abundance of biological data. The prerequisite for the course is basic knowledge of UNIX; some scripting experience is helpful. Lectures and problem sets from previous years that cover this background material are available online and students can study this material before starting the course.
The course teaches Perl, a scripting language that is easy to learn and efficient to use. Perl also has a vast array of ready-built modules such as Bioperl that are designed to solve common biological problems. We start with a week of introductory coding and continue with a survey of available biological libraries and practical topics in bioinformatics, taught by invited experts and end with a final group project. Formal instruction is provided on every topic. Students also 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. They will learn how to design, construct and run powerful and extensible analysis pipelines in a straightforward manner. Final projects have formed the basis of publications as well as public biological websites (see, for example: http://bio.perl.org/wiki/Deobfuscator). The students are provided with a library of reference books that they will take home with them. 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 2013 course included:
Scott Cain, Brian Haas, Tomas Marques-Bonet, Barry Moore, William Pearson, Jason Stajich, Paul Thomas, Jim Tisdall
This course is supported by the National
Human Genome Research Institute