The Bioperl Toolkit: Perl Modules for the Life Sciences Export

@article{citeulike:415502, 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.[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.]}, author = {Stajich, Jason E. and Block, David and Boulez, Kris and Brenner, Steven E. and Chervitz, Stephen A. and Dagdigian, Chris and Fuellen, Georg and Gilbert, James G. and Korf, Ian and Lapp, Hilmar and Lehvaslaiho, Heikki and Matsalla, Chad and Mungall, Chris J. and Osborne, Brian I. and Pocock, Matthew R. and Schattner, Peter and Senger, Martin and Stein, Lincoln D. and Stupka, Elia and Wilkinson, Mark D. and Birney, Ewan}, citeulike-article-id = {415502}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.361602}, citeulike-linkout-1 = {http://genome.cshlp.org/content/12/10/1611.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/12/10/1611.full.pdf}, citeulike-linkout-3 = {http://www.genome.org/cgi/content/abstract/12/10/1611}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/12368254}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=12368254}, day = {1}, doi = {10.1101/gr.361602}, journal = {Genome Res.}, keywords = {bioperl, microarray, snp}, month = {October}, number = {10}, pages = {1611--1618}, posted-at = {2009-06-09 20:59:21}, priority = {4}, title = {The Bioperl Toolkit: Perl Modules for the Life Sciences}, url = {http://dx.doi.org/10.1101/gr.361602}, volume = {12}, year = {2002} }

TY - JOUR ID - citeulike:415502 L3 - citeulike-article-id:415502 N2 - 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.] IS - 10 JF - Genome Res. EP - 1618 TI - The Bioperl Toolkit: Perl Modules for the Life Sciences VL - 12 SP - 1611 KW - bioperl KW - microarray KW - snp AU - Stajich, Jason AU - Block, David AU - Boulez, Kris AU - Brenner, Steven AU - Chervitz, Stephen AU - Dagdigian, Chris AU - Fuellen, Georg AU - Gilbert, James AU - Korf, Ian AU - Lapp, Hilmar AU - Lehvaslaiho, Heikki AU - Matsalla, Chad AU - Mungall, Chris AU - Osborne, Brian AU - Pocock, Matthew AU - Schattner, Peter AU - Senger, Martin AU - Stein, Lincoln AU - Stupka, Elia AU - Wilkinson, Mark AU - Birney, Ewan PY - 2002/10/01/ UR - http://dx.doi.org/10.1101/gr.361602 ER -