BioJava is a mature free and open-source project that provides a framework for processing biological data.

BioJava provides tools/packages/modules/components

for parsing common file formats,

for manipulating sequences and 3D structures,

and powerful analysis and statistical routines.

BioJava is available freely under the terms of version 2.1 of the GNU Lesser General Public License (LGPL) from http://biojava.org/.

Here we present the latest BioJava release (version 1.6, released on 13 Apr 2008) which provides improvements in the packages for phylogenetic trees, processing PDB files, and genetic algorithms.

As a free and open-source project, BioJava is developed by volunteers coordinated by the Open Bioinformatics Foundation (OBF) and is one of several Bio* toolkits (Mangalam, 2002). Over the past eight years, the BioJava has brought together nearly fifty different code contributors, hundreds of mailing list subscribers, and several wiki contributors. All code is distributed under version 2.1 of the GNU Lesser General Public License (LGPL) license (Free Software Foundation, Inc., 1999). All wiki documentation is made available online under version 1.2 of the GNU Free Documentation License (Free Software Foundation, Inc., 2000).

BioJava has been used in a number of real-world applications, including Bioclipse (Spjuth et al., 2007), BioWeka (Gewehr et al., 2007), Cytoscape (Shannon et al., 2003), and Taverna (Oinn et al., 2004), and been referenced in over 50 published studies. A list of these can be found on the BioJava website.

The latest BioJava release (version 1.6, released on 13 Apr 2008) offers more functionality and stability over the previous official releases. The phylogenomics package was improved and expanded by our 2007 Google Summer of Code (GSOC'07) student Boh-Yun Lee. It now contains fully-functional Nexus and Phylip parsers, and tools for calculating UPGMA and Neighbour Joining, Jukes-Kantor and Kimura Two Parameter, and MP. The PDB file parser was improved by Jules Jacobsen for better dealing with PDB header records. Andreas Dräger provided several patches for improving the Genetic Algorithm modules. The version 1.6 release also contains numerous bug fixes and documentation improvements.

As a mature project, BioJava faces several challenges:

how one deals with a large established code base

what happens when committers move on, get married, have kids, etc.

how difficult it is to deprecate and remove existing code

evolutionary vs. revolutionary changes [1]

the "second system" problem [2]

To this end...

the BioJava3 use case & refactoring/redesign criteria gathering process

At least one prior attempt, while technically sufficient, was unable to garner community support.

http://biojava.org/wiki/BioJava3_Proposal

http://biojava.org/wiki/BioJava3_Design

http://incubator.apache.org/learn/rules-for-revolutionaries.html

http://www.joelonsoftware.com/articles/fog0000000069.html