BOSC finishes and I weep as I miss it already

 Posted on June 28, 2003  |  brad

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. [Read More]

They let me into Australia, and this is what I saw

 Posted on June 28, 2003  |  brad

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. [Read More]

Montreal BioJava Bootcamp Announced

 Posted on June 27, 2003  |  dag

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]

BioJava 1.3 Released

 Posted on June 18, 2003  |  dag

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]

The Open Biological Database Access (OBDA) introduction for BioPerl

 Posted on June 12, 2003  |  heikki

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]