Perl/BioPerl--Biologists’ Perspective
Perl/BioPerl--Biologists’ Perspective
Day 1, Perl basics
Slides
Sample scripts
1, first perl script
2,1 variable--scalar,
2,2 array
2,3 hash
3, basic input/output
4, file I/O
5, loop control and conditional test
6, regular expression
7, subroutine
8, reference
Day 2, BioPerl basics
Slides
1, Sequence I/O and remote blast
2, retrieve sequences from GenBank
3, Align sequences by Clustalw
I thank all participants for their attendance as well as critics for the workshop. In future there will be possibly for further developing it.
I gradually realized the need for learning Perl and BioPerl among Biologists, together with the increasing demand for computational capacity under the revolutionary change in Biology because of Next-Generation-Sequencing techniques. I started to use Perl during my internship in 2010 at MPI Bremen where I learned Perl/BioPerl myself and assembled a successful pipeline, I also noticed that the focus of getting started with Perl for Biologists can be quite different--we do not really need to know all details about perl and we do not need to write a thousand line code--we simply need those stuff which are needed for biological purposes.
As a result of this, 12-13 January I organized a workshop that introduce Perl and Bioperl programming for Biologists in MPI Ploen. And despite the inexperience and time limitation, we managed to introduced the essential concepts and have writen a sample sequence analysis pipeline. This workshop has been repeated in Jan 2013 and will probably go on regularly.
I organized the slides and sample scripts with detailed explanation and hope this would benefit more biologists.