From HP-SEE Wiki

Latest revision as of 23:15, 24 April 2012

Information

• Web site: http://www.bioperl.org/
• Described version: 1.6.1
• Licensing: Dual - Perl Artistic License or GNU General Public License v3
• User documentation: http://www.bioperl.org/wiki/Category:Documentation
• Download: http://www.bioperl.org/wiki/Getting_BioPerl#BioPerl_Releases
• Source code: http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz

Authors/Maintainers

Bioperl developers: bioperl-l@bioperl.org

Summary

BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the BioPerl-live repository consist of the core of the functionality of BioPerl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules. Bioperl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS). On the other hand, Bioperl does provide reusable Perl modules that facilitate writing Perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, BioPerl enables one to develop scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.

Features

• Listed features

Architectural/Functional Overview

• high level design info, how it works, performance - may be a link, or several links

Usage Overview

• Installation on Unix and on Windows
• HowTo
• Tutorial and tutorial documents

Dependacies

• Unix
  • Perl 5.6.1 or later; version 5.8 or greater is recommended.
  • make. For Mac OS X, this requires installing the Xcode Developer Tools.
• Windows
  • ActivePerl >= 5.8.8.819

other dependencies

HP-SEE Applications

• DeepAligner (Deep sequencing for short fragment alignment) [1]
• DiseaseGene (In-silico Disease Gene Mapper) [2]

Resource Centers

• RCs supporting it (with version number if not the same as above)

Usage by other projects and communities

• If any

Recommendations for Configuration and Usage

Need to be installed to user space.