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.
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]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
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?
The Open Biological Database Access (OBDA) System was designed so that one could use the same application code to access data from all three of the database types by simply changing a few lines in a “configuration file”. This makes application code more portable and easier to maintain.
[Read More]Mark writes:
The tutorial site BioJava in Anger has been updated so the code examples reflect the new APIs in the upcomming BioJava 1.3 release. Take a peek at http://bioconf.otago.ac.nz/biojava