The Bioperl toolkit: Perl modules for the life sciences

Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G., Korf, I., Lapp, H., Lehvaslaiho, H., Matsalla, C., Mungall, C. J., Osborne, B. I., Pocock, M. R., Schattner, P., Senger, M., Stein, L. D., Stupka, E., Wilkinson, M. D., Birney, E. (October 2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Research, 12 (10). pp. 1611-8. ISSN 10889051 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/12368254
DOI: 10.1101/gr.361602

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.

Item Type: Paper
Uncontrolled Keywords: Algorithms Animals Biological Sciences/*methods/trends Computational Biology/*methods/trends Computer Graphics Database Management Systems Databases, Genetic Humans Internet Online Systems Software Software Design Systems Integration
Subjects: bioinformatics
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > computers > computer software
CSHL Authors:
Communities: CSHL labs > Stein lab
Depositing User: Matt Covey
Date: October 2002
Date Deposited: 30 Oct 2013 19:30
Last Modified: 30 Oct 2013 19:30
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28790

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