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.
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.
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.
- API docs (BioJava version 1.6-rc1)
- API docs (BioJava version 1.5)
- API docs (BioJava version 1.4)
- API docs (BioJava version 1.3)
The BioJava tutorial is here
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.
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:  -- 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.