prlic bio java bosc2009
TRANSCRIPT
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...