Prlic Bio Java Bosc2009

•

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bosc

Technology Education

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 • 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

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 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

Modularization

Instead of one big
“Monster” project...

Multiple smaller
modules

Little dependencies between
each other

Trying not to break backwards-
compatibility

Smaller installations

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

How to support?

• By answering emails on the public mailing
lists
• Create / maintain documentation in wiki
• Providing new modules / submit patches for
existing ones

Acknowledgments
• ~10 years of development
• 49 contributors...

Thanks to the Open Bioinformatics
Foundation / Chris Dagdigian for hosting

BioJava User Meeting

• BOF session later on...

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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

6. Currently ongoing...

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...

Prlic Bio Java Bosc2009

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