BioJava 5.0.0 is out

 Posted on April 9, 2018  |  josemduarte

BioJava 5.0.0 was released on the 23rd of March 2018. This represents a major milestone that brings more consolidation and reorganisation of modules. This is the first release to be based on Java 8, bring in your lambdas and stream API calls! The release represents work done in the last 2 years, alpha releases were available for quite some time and now this makes all the changes officially public. Some major refactoring occurred in the biojava-structure module. [Read More]

New BioJava Logo Design Competition

 Posted on June 14, 2016  |  andreas

BioJava is organizing a design competition to come up with a new logo. Anybody can participate: The logo should look modern and be better than the current one (yellow circle) The logo should be able to be rendered as a favicon, as well as large (e.g. on a t-shirt). Designs that come in two (or multiple) sizes are ok. Logos shall not look similar in any way to the trademarked Java programming language logo. [Read More]

Sanger FASTQ format and the Solexa/Illumina variants

 Posted on December 17, 2009  |  peterc

I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants Peter J. A. Cock ( Biopython), Christopher J. Fields ( BioPerl), Naohisa Goto ( BioRuby), Michael L. Heuer ( BioJava) and Peter M. Rice ( EMBOSS). Nucleic Acids Research, doi:10. [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. [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]