BioJava 2009
An Open Source Framework
for Bioinformatics
http://www.biojava.org
Andreas Prlić BOSC 2009

What is BioJava?
• Java framework for processing of biological
data
• Analysis and statistics routines
• Parse common file formats
• Manipulate sequences and 3D structures
• Goal: facilitate rapid application
development

Major Features
• Alphabets and Symbols • Dynamic Programming
and Substitution Matrices
• Sequence manipulation
• User Interfaces
• Translation
• BioSQL and Sequence
• Sequence I/O Databases
• Annotations • Genetic Algorithms
• Locations and Features • Protein Structure
• Blast and Fasta parsing • Phylogenetics
• Counts and Distributions

What is new in 2009?
• New version - BioJava 1.7
• Improved support for 3D structures, PDB
headers, mmCif, Chemical Component
Dictionary
• Numerous bug fixes and minor
improvements
• BioGroovy

RCSB Viewers
open sourced
Viewer uses symmetry
transformation to build the
biological molecule on the fly
1sva
Simian virus 40
Molecular Biology Toolkit: J.L. Moreland, A.Gramada, O.V. Buzko, Q. Zhang and P.E. Bourne, Bioinformatics 2005
Protein Workshop: John Beaver
Ligand Explorer: Cindy Zhang
Refactoring: Rick Berger

Currently ongoing...

Modularization
Instead of one big
“Monster” project...

Multiple smaller
modules
Little dependencies between
each other
Trying not to break backwards-
compatibility
Smaller installations

Modules already in SVN
• biojava-core
• biojava-structure
• biojava-phylo
• biojava-blast
• biojava-alignment
• biojava-das
• biojava-ws-biolit

Planning...
• Support for frequently used web services
• biojava-ws-blast
• biojava-ws-*
• biojava-biosql

Each module
• Will contain its own
• source
• demos
• Junit tests
• Documentation in Wiki - Cookbook

Migration to
Maven
•Changing the build system
•Easier deployment of
modules
•Dependency management
•Easy to make releases

Join us
• biojava-l
• biojava-dev
• Get the source code:
http://www.biojava.org
• Open access under LGPL

How to support?
• By answering emails on the public mailing
lists
• Create / maintain documentation in wiki
• Providing new modules / submit patches for
existing ones

Acknowledgments
• ~10 years of development
• 49 contributors...
Thanks to the Open Bioinformatics
Foundation / Chris Dagdigian for hosting

BioJava User Meeting
• BOF session later on...