Prlic Bio Java Bosc2009
2 likes710 views
BioJava is an open source Java framework for processing biological data. It provides tools for analyzing and manipulating sequences, structures, and other biological data. The latest version, BioJava 1.7, includes improved support for 3D structures and modularization into separate modules. The project aims to facilitate rapid bioinformatics application development and is supported by an active developer community.
Prlic Bio Java Bosc2009
- 1. BioJava 2009 An Open Source Framework for Bioinformatics http://www.biojava.org Andreas Prlić BOSC 2009
- 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. 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. 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. 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
- 7. Modularization Instead of one big “Monster” project...
- 8. Multiple smaller modules Little dependencies between each other Trying not to break backwards- compatibility Smaller installations
- 9. Modules already in SVN • biojava-core • biojava-structure • biojava-phylo • biojava-blast • biojava-alignment • biojava-das • biojava-ws-biolit
- 10. Planning... • Support for frequently used web services • biojava-ws-blast • biojava-ws-* • biojava-biosql
- 11. Each module • Will contain its own • source • demos • Junit tests • Documentation in Wiki - Cookbook
- 12. Migration to Maven •Changing the build system •Easier deployment of modules •Dependency management •Easy to make releases
- 13. Join us • biojava-l • biojava-dev • Get the source code: http://www.biojava.org • Open access under LGPL
- 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. Acknowledgments • ~10 years of development • 49 contributors... Thanks to the Open Bioinformatics Foundation / Chris Dagdigian for hosting
- 16. BioJava User Meeting • BOF session later on...