The “Biojava in Anger: A Tutorial and Recipe Book for Those in a Hurry” posted online at http://www.biojava.org/docs/bj_in_anger/index.htm has been translated into French and Japanese
About the OBF
The Open Bioinformatics Foundation (OBF) is a non-profit, volunteer-run group that promotes open source software development and Open Science within the biological research community. Membership in the OBF is free and open to anyone who wants to help promote open source or open science in a biological field.
OBF runs the annual Bioinformatics Open Source Conference (BOSC).
BOSC 2025 took place July 21-22, 2025, in Liverpool, UK (as part of ISMB/ECCB 2025). BOSC 2026 will be part of ISMB 2026 in Washington, DC.
OBF Event Awards
The OBF Event Fellowship program aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community.
new restriction analysis classes
Rob Edwards and Heikki Lehvaslaiho have been writing new restriction analysis classes. These will eventually replace the long serving Bio::Tools::RestrictionEnzyme by Steve Chervitz. The first working versions are in CVS.
A UML graph shows the class relationships. A more verbose overview is below.
[Read More]
Bioperl 1.2.2 released
This is a bug fix release from the stable branch.
The Bioperl release 1.2.2 is available at http://www.bioperl.org/DIST/bioperl-1.2.2.tar.gz and is propagating around CPAN now.
Bioperl-run is a collection of modules that wrap bioinformatics applications to allow running them from bioperl. The release cycle of bioperl-run follows the core. The latest bioperl-run release is therefore at: http://www.bioperl.org/DIST/bioperl-run-1.2.2.tar.gz
[Read More]BOSC'2003 Pictures are online
Our “Bioinformatics Open Source Conference” was held in Brisbane, Australia in conjunction with the larger ISMB'2003 meeting. It was quite successful — 96 attendees, wireless internet, BOF rooms and 30+ presentations over 2 days.
Pictures are online here: http://gallery.open-bio.org/
Release candidate 1.2.2 available
A possible release candidate for BioPerl 1.2.2 is now available for download: http://bioperl.org/DIST/bioperl-1.2.2rc1.tar.gz
Please download and give it a test. New aditions, features and fixes are in the “Changes” file.
BOSC finishes and I weep as I miss it already
BOSC always comes and goes so fast. I am a melancholy kind of guy so whenever things finish up I get a little misty eyed with regrets at the things I could have done and the people I could have met. But it was all so great it makes me smile with the understanding of the entire world. Plus weeping really gets you the women – makes you look quite sensitive. And I am all about sensitivity. But before I got into this mindset, I tried to write down what happened. Read and feel my joy.
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They let me into Australia, and this is what I saw
If you are not lucky enough to be here in wonderfully beautiful Brisbane with beaches next to the river and where every man and woman is a perfect physical specimen, then you can read all about BOSC colored through my mind. Enjoy.
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Montreal BioJava Bootcamp Announced
BioneQ, the Quebec Bioinformatics Network, is organizing the first North American BioJava Bootcamp from August 18th to 22nd. We have invited Matthew Pocock to come to Montreal to present the material that has been presented to the European Bootcamps for quite some time now. On the agenda (preliminary):
-Sequence I/O and manipulations; -BLAST and FASTA parsing; -Using databases with BioJava; -Intro to Sequence GUI.
The bootcamp will be at the Universite de Montreal and the registration fee is $250US. If you are interested, use the following link to register:
[Read More]BioPerl workshop materials online
Heikki has converted some Bioperl workshop materials to a web slide show that is available here:
BioJava 1.3 Released
Thomas Down writes:
After a long series of pre-releases (and many bug fixes), I’ve just finished building BioJava 1.30. Source, binaries, and javadocs can all be found at:
http://www.biojava.org/download/
As with the pre-releases, separate binaries are available for java platform releases 1.3 and 1.4. The 1.4 releases include some extra features which depend on jdk1.4 extensions such as the java.nio package.
Highlights of this release include:
- Packed storage of sequence data in memory
- Better support for the OBDA database access standards
- Improvements to the parsers for output from tools like blast and fasta.
- Many enhancements to the FeatureFilter system.
[Read More]