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Prlic Bio Java Bosc2009

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Prlic Bio Java Bosc2009

  1. 1. BioJava 2009 An Open Source Framework for Bioinformatics http://www.biojava.org Andreas Prlić BOSC 2009
  2. 2. 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
  3. 3. 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
  4. 4. 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
  5. 5. 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
  6. 6. Currently ongoing...
  7. 7. Modularization Instead of one big “Monster” project...
  8. 8. Multiple smaller modules Little dependencies between each other Trying not to break backwards- compatibility Smaller installations
  9. 9. Modules already in SVN • biojava-core • biojava-structure • biojava-phylo • biojava-blast • biojava-alignment • biojava-das • biojava-ws-biolit
  10. 10. Planning... • Support for frequently used web services • biojava-ws-blast • biojava-ws-* • biojava-biosql
  11. 11. Each module • Will contain its own • source • demos • Junit tests • Documentation in Wiki - Cookbook
  12. 12. Migration to Maven •Changing the build system •Easier deployment of modules •Dependency management •Easy to make releases
  13. 13. Join us • biojava-l • biojava-dev • Get the source code: http://www.biojava.org • Open access under LGPL
  14. 14. How to support? • By answering emails on the public mailing lists • Create / maintain documentation in wiki • Providing new modules / submit patches for existing ones
  15. 15. Acknowledgments • ~10 years of development • 49 contributors... Thanks to the Open Bioinformatics Foundation / Chris Dagdigian for hosting
  16. 16. BioJava User Meeting • BOF session later on...

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