Prlic Bio Java Bosc2009
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Transcript of Prlic Bio Java Bosc2009
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BioJava 2009An Open Source Framework
for Bioinformaticshttp://www.biojava.org
Andreas Prlić BOSC 2009
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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
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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
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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
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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
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Currently ongoing...
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Modularization
Instead of one big “Monster” project...
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Little dependencies between each other
Trying not to break backwards-compatibility
Smaller installations
Multiple smaller modules
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Modules already in SVN• biojava-core
• biojava-structure
• biojava-phylo
• biojava-blast
• biojava-alignment
• biojava-das
• biojava-ws-biolit
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Planning...
• Support for frequently used web services
• biojava-ws-blast
• biojava-ws-*
• biojava-biosql
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Each module
• Will contain its own
• source
• demos
• Junit tests
• Documentation in Wiki - Cookbook
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Migration to Maven
•Changing the build system •Easier deployment of modules•Dependency management•Easy to make releases
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Join us
• biojava-l
• biojava-dev
• Get the source code: http://www.biojava.org
• Open access under LGPL
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• By answering emails on the public mailing lists
• Create / maintain documentation in wiki
• Providing new modules / submit patches for existing ones
How to support?
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Acknowledgments• ~10 years of development
• 49 contributors...
Thanks to the Open Bioinformatics Foundation / Chris Dagdigian for hosting
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BioJava User Meeting
• BOF session later on...