The Bioperl toolkit: Perl modules for the life sciences

Jason E. Stajich, David Block, Kris Boulez, Steven E. Brenner, Stephen A. Chervitz, Chris Dagdigian, Georg Fuellen, James G R Gilbert, Ian Korf, Hilmar Lapp, Heikki Lehväslaiho, Chad Matsalla, Chris J. Mungall, Brian I. Osborne, Matthew R. Pocock, Peter Schattner, Martin Senger, Lincoln D. Stein, Elia Stupka, Mark D. WilkinsonEwan Birney

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish
Pages (from-to)1611-1618
Number of pages8
JournalGenome Research
Volume12
Issue number10
DOIs
Publication statusPublished - Oct 1 2002

ASJC Scopus subject areas

  • Genetics

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    Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G. R., Korf, I., Lapp, H., Lehväslaiho, H., Matsalla, C., Mungall, C. J., Osborne, B. I., Pocock, M. R., Schattner, P., Senger, M., Stein, L. D., Stupka, E., ... Birney, E. (2002). The Bioperl toolkit: Perl modules for the life sciences. Genome Research, 12(10), 1611-1618. https://doi.org/10.1101/gr.361602