BioJava 3.0.8 released

 BioJava 3.0.8 was released on March 25th 2014 and is available from

http://biojava.org/wiki/BioJava:Download as well as from the

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

This release would not have been possible without contributions from

13 developers, thanks to all for their support!

BioJava 3.0.8 includes a lot of new features as well as numerous bug fixes and improvements.

New Features:

•  new Genbank writer
•  new parser for Karyotype file from UCSC
•  new parser for Gene locations from UCSC 
•  new parser for Gene names file from genenames.org
•  new module for Cox regression code for survival analysis
•  new calculation of accessible surface area (ASA)
•  new module for parsing .OBO files (ontologies)
•  improved representation of SCOP and Berkeley-SCOP classifications

 

For a detailed comparison see here:

https://github.com/biojava/biojava/compare/biojava-3.0.7...biojava-3.0.8

For the next release we are planning some refactoring and removal of code that has been deprecated for a long time. As such the next release will be named 3.1.0.

About BioJava:

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.

Happy BioJava-ing,

Andreas

BioJava 2012 paper published

Today the latest BioJava paper was published, describing the BioJava version 3 series .

Thanks to all developers for their contributions, it would not have been possible without them!

Abstract:

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref

PDF:

http://bioinformatics.oxfordjournals.org/cgi/reprint/bts494?ijkey=BzJOy9GgM2XNw07&keytype=ref

Citation:

BioJava: an open-source framework for bioinformatics in 2012

Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius
Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock
Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L.
Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis

Bioinformatics 2012; doi: 10.1093/bioinformatics/bts494

BioJava at at Google Summer of Code 2012

The Open Bioinformatics foundation as an umbrella organisation for
BioJava has been accepted to participate in this year's Google Summer
of Code. 

This means we will again be able to offer mentoring through BioJava
this year. Accepted students will get a stipend of 5,000$ from Google.
Participation is possible from most countries in the world, as long as
you are eligible to work in the country in which you'll reside
throughout the duration of the program.

If you are interested in working on a BioJava related project, now is
the time to start preparing and discussing your proposals. For the
last two years we had many applications for the projects proposed by
mentors. If you want to distinguish your application I recommend to
propose your own  project. Don't forget to discuss any proposal with
us before you submit them. We will try to provide feedback and match
you with a suitable Mentor.

Also see http://biojava.org/wiki/Google_Summer_of_Code and Google's
FAQs: http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs

The student application deadline is April 6th. Google will announce
which proposals got accepted on April 23rd.

Google Summer of Code 2010

Our (the Open Biology Foundation's) application for the Google Summer of Code has been accepted. http://socghop.appspot.com/gsoc/program/accepted_orgs/google/gsoc2010

I am offering to mentor a project to develop an All-Java Multiple Sequence Alignment algorithm as part of the BioJava project.

If you are an interested and skilled student, take a look at the project description, and if you think you are up for the challenge, send me an email with your application.

http://biojava.org/wiki/Google_Summer_of_Code