RT Journal
A1 Stajich, Jason E.
A1 Block, David
A1 Boulez, Kris
A1 Brenner, Steven E.
A1 Chervitz, Stephen A.
A1 Dagdigian, Chris
A1 Fuellen, Georg
A1 Gilbert, James G.R.
A1 Korf, Ian
A1 Lapp, Hilmar
A1 Lehväslaiho, Heikki
A1 Matsalla, Chad
A1 Mungall, Chris J.
A1 Osborne, Brian I.
A1 Pocock, Matthew R.
A1 Schattner, Peter
A1 Senger, Martin
A1 Stein, Lincoln D.
A1 Stupka, Elia
A1 Wilkinson, Mark D.
A1 Birney, Ewan
T1 The Bioperl Toolkit: Perl Modules for the Life Sciences
JF Genome Research 
JO Genome Research 
YR 2002 
FD October 01 
VO 12 
IS 10 
SP 1611 
OP 1618 
DO 10.1101/gr.361602 
UL http://genome.cshlp.org/content/12/10/1611.abstract 
AB The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.[Supplemental material is available online at www.genome.org. Bioperl is available as open-source software free of charge and is licensed under the Perl Artistic License (http://www.perl.com/pub/a/language/misc/Artistic.html). It is available for download at http://www.bioperl.org. Support inquiries should be addressed to bioperl-l@bioperl.org.]