Current events

From BioJava

BOSC 2008 Presentation

Michael presented BioJava at this year's ISMB in Toronto. For the presentation and discussion see BOSC2008_Presentation.

BioJava 1.6 released

Version 1.6 release announcement to biojava-dev and biojava-l

Date: Sun, 13 Apr 2008 19:02:41 +0100 From: Andreas Prlic To: biojava-dev at biojava.org, biojava-l at biojava.org Subject: [Biojava-dev] biojava 1.6 released

Biojava 1.6 has been released and is available from BioJava:Download

Biojava 1.6 offers more functionality and stability over the previous official releases. BioJava now depends on Java 1.5+. We highly recommend you to upgrade as soon as possible.

In detail, the phylo package org.biojavax.bio.phylo was improved and expanded by our GSOC'07 student Boh-Yun Lee. It now contains fully- functional Nexus and Phylip parsers, and tools for calculating UPGMA and Neighbour Joining, Jukes-Kantor and Kimura Two Parameter, and MP. It uses JGraphT to represent parsed trees.

The PDB file parser was improved by Jules Jacobsen for better dealing with PDB header records. Andreas Draeger provided several patches for improving the Genetic Algorithm modules. Additionally this release contains numerous bug fixes and documentation improvements.

Thanks to the entire biojava community for making this possible!

Happy Biojava-ing,

Andreas

Migration from CVS to Subversion

(Jan. 2008) BioJava has moved the source repository from CVS to Subversion (SVN). See CVS_to_SVN_Migration

BOSC 2007 Presentation

For those of you who can't be in Vienna for Richard's biojava presentation for BOSC 2007. You can view the pdf here.

NESCent Phyloinformatics and the Google Summer of Code

BioJava is hosting a student from the Google Summer of Code who is planning on developing and extending the phyloinformatics APIs in BioJava. Bohyun Lee aims to create parsers for the common phyloinformatics file formats (Nexus etc.), provide an object model for storing trees, and provide API methods for manipulating and querying those trees.

The project is part of the NESCent Phyloinformatics group of projects.

Bohyun will be documenting progress and discussing plans as the project progresses. Please feel free to chip in with your own comments and suggestions.