BioJava 2009An Open Source Framework

for Bioinformaticshttp://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

• Sequence manipulation

• Translation

• Sequence I/O

• Annotations

• Locations and Features

• Blast and Fasta parsing

• Counts and Distributions

• Dynamic Programming and Substitution Matrices

• User Interfaces

• BioSQL and Sequence Databases

• Genetic Algorithms

• Protein Structure

• Phylogenetics

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 40Molecular Biology Toolkit: J.L. Moreland, A.Gramada, O.V. Buzko, Q. Zhang and P.E. Bourne, Bioinformatics 2005Protein Workshop: John BeaverLigand Explorer: Cindy Zhang Refactoring: Rick Berger

Currently ongoing...

Modularization

Instead of one big “Monster” project...

Little dependencies between each other

Trying not to break backwards-compatibility

Smaller installations

Multiple smaller modules

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

• By answering emails on the public mailing lists

• Create / maintain documentation in wiki

• Providing new modules / submit patches for existing ones

How to support?

Acknowledgments• ~10 years of development

• 49 contributors...

Thanks to the Open Bioinformatics Foundation / Chris Dagdigian for hosting

BioJava User Meeting

• BOF session later on...