Perl/BioPerl--Biologists’ Perspective

 
 

Day 1, Perl basics

Slides

perl work shop.pptx

Sample scripts

1, first perl script

first.pl

2,1 variable--scalar,

scalar.pl

2,2 array

array.pl

2,3 hash

hash.pl

3, basic input/output

input.pl

4, file I/O

fileio.pl

5, loop control and conditional test

loop.pl

6, regular expression

regularexpression.pl

7, subroutine

subroutine.pl

8, reference

reference.pl

Day 2, BioPerl basics

Slides

Perl workshop day2.pptx

1, Sequence I/O and remote blast

bioseqio_blast.pl

2, retrieve sequences from GenBank

retrieve.pl

3, Align sequences by Clustalw

clustal.pl





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.