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. Bio::Restriction::Enzyme class knows (almost) everything there to know about restriction enzymes.
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.
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.
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 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.
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.
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.
Heikki has converted some Bioperl workshop materials to a web slide show that is available here: http://www.ebi.ac.uk/~lehvasla/bioperl/
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.
Rhett Sutphin provides a mini-primer and some example code that shows how to view Chromatogram files with java.
Do you need to access sequences from multiple places? Would you like to easily retrieve your own local sequences from indexed flat files, all other sequences on species X from department wide raletional database and the rest from global internet servers?