Bio-perl

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[edit] Introduction

This is the BioPerl project's community documentation site. You can read up on Getting BioPerl, Installing BioPerl, and Getting Started using the toolkit. Advanced BioPerl covers a number of topics once you've got the hang of things. Also use the Frequently Asked Questions, HOWTOs, and the BioPerl Tutorials as starting place for learning about the toolkit's components.

More specific information for developers can be found here and on the sidebar.

There is a short History of BioPerl with background on the project and Lincoln Stein's article on How Perl Saved the Human Genome Project.

See what BioPerl Users are using the toolkit for and what publications cite the toolkit.

The toolkit is divided into several packages, most people will only want to deal with the Core package.

• Core package provides the main parsers, this is the basic package and it's required by all the other packages (bioperl-live SVN directory)
• Run package provides wrappers for executing some 60 common bioinformatics applications (bioperl-run in SVN)
• BioPerl db package is a subproject to store sequence and annotation data in a BioSQL relational database (bioperl-db in SVN).
• Network package parses and analyzes protein-protein interaction data (bioperl-network in SVN).
• See all the available packages via Downloads page

API documentation for each module at doc.bioperl.org and each module page on this site is linked to the doc site and the CPAN perldoc documentation. There are lists of the documented Core modules, Run modules, DB modules, and Ext modules available on this site and the external API documentation.

[edit] Current Events

[edit] General

• We are now gathering comments on the proposed core module changes.
• Bioperl 1.5.2 has been released! Check the Release page for further details.
• Deobfuscator released to help navigate the API documentation better.
• We welcome new developers to help with projects in the project priority list.
• There is list of orphan modules which need a volunteer to maintain them.
• BOSC 2007 was held July 19-20, 2007 in conjunction with ISMB2007 in Vienna, Austria. BOSC 2006 was held on Aug 4-5, 2006 at ISMB 2006 in Fortaleza, Brazil.
• See the News page for latest mailing list traffic and news. Also see the RSS feeds for easy ways to subscribe to mailing list and development feeds.

[edit] Developers

• Migration to the new Subversion is complete. Information is now available on the BioPerl migration to Subversion and using Subversion with BioPerl.
• Feature/Annotation changes introduced prior to the 1.5 release have been rolled back in preparation for a new stable release. The Rollback page has the detailed notes for the rollback; currently all tests related to this pass.
• We are planning tentative steps in making GFF3-compatible output for the various BioPerl classes. See the code audit page for details; contribute by discussing suggestions on the mail list and donating code!
• Perl 5.10 has been released. We have a Perl 5.10 compatibility page which tracks bugs and other issues related to using Perl 5.10 and BioPerl.

BioPerl is distributed under the Perl Artistic License. For more information on what the means for users and developers using the toolkit see more information about licensing BioPerl.