Biojava on Open Bioinformatics Foundation

BioJava 5.0.0 is out

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 09 Apr 2018 17:37:14 +0000

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. The data model to deal with macromolecular structures has been adapted to be closer to the mmCIF data model. Other improvements in biojava-structure are support for MMTF format and improved symmetry detection code.

See the full release notes or browse the official API documentation.

New BioJava Logo Design Competition

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 14 Jun 2016 17:47:52 +0000

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. This means no coffee cups in any way.

Deadline: Deadline for submissions is July 4th.

Announcement of Winner: The winner of the new logo competition will be announced during BOSC 2016.

Prize: We will print t-shirts with the new logo and the designer will get a free t-shirt.

If the designer of the winning new logo will be attending ISMB 2016, the attending BioJava developers will take the winner out for dinner.

BioJava will carry the new logo on its homepage and GitHub Profile

Details: For full details of the competition and how to make a submission please view here:

https://github.com/biojava/logo Result Update:

As announced via the mailing list and at BOSC 2016, the winning logo was by Aleix Latifa:

BioJava 3.0.4 released

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 23 May 2012 16:18:11 +0000

BioJava 3.0.4 has been released and is available from http://www.biojava.org/wiki/BioJava:Download as well as from the

BioJava maven repository at http://www.biojava.org/download/maven/ .

- This is mainly a bug fix release addressing issues with the protein

structure and disorder modules

- One new feature: SCOP data can now be accessed from either the original SCOP site in the UK (v. 1.75) or from Berkeley (v. 1.75A) .

Sanger FASTQ format and the Solexa/Illumina variants

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 17 Dec 2009 16:28:55 +0000

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:10.1093/nar/gkp1137

This will hopefully serve as a reference describing the original standard Sanger FASTQ, and the two variants from Solexa/Illumina, and how to inter-convert between them.

'biojava in anger' translated to French and Japanese

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 28 Jul 2003 02:30:53 +0000

The “Biojava in Anger: A Tutorial and Recipe Book for Those in a Hurry” posted online at http://www.biojava.org/docs/bj_in_anger/index.htm has been translated into French and Japanese

Montreal BioJava Bootcamp Announced

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 27 Jun 2003 06:24:36 +0000

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:

http://132.204.90.239/bioneq/biojava_workshop.jsp

Please paste in your CV for evaluation of programming experience/knowledge. Places are quite limited (20) so register soon.

BioJava 1.3 Released

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 18 Jun 2003 06:09:12 +0000

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.

Please check out the javadocs for information on these and other new features.

I’d also like to take this opportunity to recomment the excellent BioJava in Anger website, which is now hosted on biojava.org:

http://www.biojava.org/docs/bj_in_anger/index.htm

Thanks to everyone who has made this release possible:

Aroul Ramadass Brian Gilman Brian King Cambridge Antibody Technology (CAT) David Allen David H. Klatte, Ph.D. David Huen David Waring Ewan Birney Francois Pepin Gerald Loeffler Greg Cox Hanning Ni Jason Stajich Kalle Naslund Keith James Kim Rutherford Lachlan Coin Laurent Jourdren Leen Ammeraal Lei Lai Mark Schreiber Martin Senger Matthew Pocock Mayo Foundation Michael Heuer Michael Jones Moses Hohman Nimesh Singh Paul Seed Rhett Sutphin Robin Emig Ron Kuhn Russell Smithies Samiul Hasan Thad Welch Thomas Down

I hope you all find it useful,

Thomas.

40+ biojava tutorials available

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 08 Jan 2003 06:43:51 +0000

Mark Schreiber has posted more than 40 tutorials on using “biojava in anger” at http://bioconf.otago.ac.nz/biojava/