PhD student Gladys Andino recently attended the Programming for Biology course at Cold Spring Harbor Laboratory, New York. This 15-day course focused on scripting using the Perl programming language to enable biologists to analyze next generation sequencing DNA and RNA data.
The first week focused on familiarity with Unix and the basics of Perl, as well as ready-built modules like Bioperl. Introductory coding lectures were followed by sessions of problem solving sets. Each session allowed continuation of exploring different biological libraries and practical bioinformatics tools such as BLAST, genome and transcriptome assemblers, as well as SNP's discovery software.
The second week combined intensive lectures and hands-on workshops, which focused on constructing and running powerful and extensible analysis pipelines in a straightforward manner, allowing opportunities to apply available bioinformatics tools.
The course wrapped up with final projects, in which attendees could propose their own research problems.
Even though Superstorm Sandy hit the area while Gladys was there, she still came away from it with a very positive impression. In her words: "Despite Hurricane Sandy, I consider the course a great learning experience where new friendships and collaborations were made. I have to say that the long-hour days were all worthy!"