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The Bioperl toolkit: Perl modules for the life sciences.

Publication ,  Journal Article
Stajich, JE; Block, D; Boulez, K; Brenner, SE; Chervitz, SA; Dagdigian, C; Fuellen, G; Gilbert, JGR; Korf, I; Lapp, H; Lehväslaiho, H ...
Published in: Genome research
October 2002

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.

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Published In

Genome research

DOI

EISSN

1549-5469

ISSN

1088-9051

Publication Date

October 2002

Volume

12

Issue

10

Start / End Page

1611 / 1618

Related Subject Headings

  • Systems Integration
  • Software Design
  • Software
  • Online Systems
  • Internet
  • Humans
  • Databases, Genetic
  • Database Management Systems
  • Computer Graphics
  • Computational Biology
 

Citation

APA
Chicago
ICMJE
MLA
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Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., … 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
Stajich, Jason E., David Block, Kris Boulez, Steven E. Brenner, Stephen A. Chervitz, Chris Dagdigian, Georg Fuellen, et al. “The Bioperl toolkit: Perl modules for the life sciences.Genome Research 12, no. 10 (October 2002): 1611–18. https://doi.org/10.1101/gr.361602.
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome research. 2002 Oct;12(10):1611–8.
Stajich, Jason E., et al. “The Bioperl toolkit: Perl modules for the life sciences.Genome Research, vol. 12, no. 10, Oct. 2002, pp. 1611–18. Epmc, doi:10.1101/gr.361602.
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome research. 2002 Oct;12(10):1611–1618.

Published In

Genome research

DOI

EISSN

1549-5469

ISSN

1088-9051

Publication Date

October 2002

Volume

12

Issue

10

Start / End Page

1611 / 1618

Related Subject Headings

  • Systems Integration
  • Software Design
  • Software
  • Online Systems
  • Internet
  • Humans
  • Databases, Genetic
  • Database Management Systems
  • Computer Graphics
  • Computational Biology