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 will be July 21-22, 2025, in Liverpool, UK (as part of ISMB/ECCB 2025). BOSC 2024 took place July 15-16, 2024, as part of ISMB 2024 in Montréal, Canada.
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.
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]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]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/
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.
Heikki has converted some Bioperl workshop materials to a web slide show that is available here:
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]Rhett Sutphin provides a mini-primer and some example code that shows how to view Chromatogram files with java.
His full posting can be read here: http://pw600a.bioperl.org/pipermail/biojava-l/2003-June/003896.html
