Current events
From BioJava
Google Summer of Code
BioJava is participating in the Google Summer of Code. We are currently accepting student applications. For more info see here Google_Summer_of_Code
BioJava Hackathon 2010
The BioJava Hackaton will take place at the Genome Campus in Hinxton, Cambridge, U.K. from Jan. 19th-22nd. For more info see BioJava:Hackathon2010.
BioJava at BOSC 2009
There will be a BioJava talk at BOSC2009 in Stockholm, Sweden. We will also have a BioJava user meeting as part of the Birds of a Feather session on Sunday there.
BioJava 1.7 has been released
Sun, Apr 12, 2009 at 7:47 PM
Biojava 1.7 has been released and is available from BioJava:Download
BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats, and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language.
Besides numerous bug fixes and stability improvements, a lot of development has been going on in the protein structure modules. BioJava now provides a framework for parsing mmCif files. The parsing of PDB header information has been improved and a new tool to read the Chemical component dictionary is in place. Biojava 1.7 offers more functionality and stability over the previous official releases. We highly recommend you to upgrade as soon as possible.
Thanks to all contributors for making this release possible.
Happy Biojava-ing,
Andreas
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.
