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== Bugs and Requests for enhancement ==
 
== Bugs and Requests for enhancement ==
 
BioJava probably contains the odd bug, who would have thought!! We make use of the [http://www.bugzilla.org Bugzilla] bug reporting and tracking system. You can use it to [http://bugzilla.open-bio.org/ submit] a new bug or request for enhancement or to [http://bugzilla.open-bio.org/ view] open bugs or known issues.
 
BioJava probably contains the odd bug, who would have thought!! We make use of the [http://www.bugzilla.org Bugzilla] bug reporting and tracking system. You can use it to [http://bugzilla.open-bio.org/ submit] a new bug or request for enhancement or to [http://bugzilla.open-bio.org/ view] open bugs or known issues.
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We are currently working on a design proposal for a new version of BioJava. You can read it [[BioJava3_Design|here]].
  
 
== Documentation ==
 
== Documentation ==

Revision as of 11:38, 25 February 2008

Contents

About BioJava

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating biological sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic programming toolkit.

BioJava is used in several real-world bioinformatics applications and has been used for bioinformatics analysis in a number of published studies.

Getting BioJava

BioJava is distributed under the terms of the GNU Lesser GPL V2.1. This means that you can use the libraries without your software being forced under either the LGPL or GPL. LGPL is not GPL.

BioJava releases can be obtained from our download area. Instructions for installing the library, and building source releases, can be found on the Getting started page.

You can also maintain an up-to-date view of BioJava using Subversion. You can obtain an anonymous checkout of biojava or browse the SVN repository. Automated builds from the latest subversion checkouts are available from http://www.spice-3d.org/cruise/

If you wish to contribute your existing code or help maintain part of the BioJava code-base, then we can supply you with a read/write account. Sign up for the biojava-dev mailing list and post a request for an account.

Bugs and Requests for enhancement

BioJava probably contains the odd bug, who would have thought!! We make use of the Bugzilla bug reporting and tracking system. You can use it to submit a new bug or request for enhancement or to view open bugs or known issues.

We are currently working on a design proposal for a new version of BioJava. You can read it here.

Documentation

Cookbook

The biojava project maintains a cookbook of examples that help you perform common tasks and get you started using biojava. The cookbook is affectionately known as Biojava in Anger. A French version is also available.

API Documentation (JavaDocs)

The following are links to API documentation autogenerated by javadoc.

BioJava Tutorial

The BioJava tutorial is here

BioJavaX Documentation

This documentation is just as much under development as the code it refers to, so use with care. It is a rough guide rather than a detailed description.

Dazzle

The Dazzle DAS server repository and documentation has been moved to a new location

Thanks

The open-bio servers reside in in a Tier 1 Boston area colocation facility. Infrastructure geeks can see pictures of the colocation cage and the new OBF servers online at this URL: [1] -- those servers also host EMBOSS FTP/CVS and mailing lists.

We would like to thank Chris Dagdigian from The Bioteam for providing and maintaining the bio* servers.


Please see documentation on customizing the interface and the User's Guide for usage and configuration help.

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