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BioJava at Google Summer of Code 2012

BioJava is participating at this years' Google Summer of Code again. Find out more about it at Google_Summer_of_Code

BioJava 3.0.3 released

BioJava 3.0.3 was released on March 16th and is available from BioJava:Download.

BioJava 3.0.3 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/ .

New Features

BioJava 3.0.3 adds several new features

- Significant improvements for the web service module (ncbi blast and hmmer web services)

- Fastq parser (ported from the biojava 1 series to version 3)

- Support for SIFTS-PDB to UniProt mapping

- Improved support for working with external protein domain definitions

- Protmod module renamed to modfinder

- Numerous improvements all over the place (several hundred commits since last release)

- We are also working on an update for the legacy biojava 1.8 series.

This release would not have been possible with contributions from numerous people, thanks to all for their support!

BioJava 3.0.2 released

BioJava 3.0.2 was released on September 2nd 2011 and is available from BioJava:Download.

BioJava 3.0.2 adds new modules and enhances the capabilities of BioJava:

- biojava3-aa-prop: This new module allows the calculation of physico chemical and other properties of protein sequences.
- biojava3-protein-disorder: A new module for the prediction of disordered regions in proteins. It based on a Java implementation of the RONN predictor.

Other noteworthy improvements:

- protein-structure: Improved handling of protein domains: Now with better support for SCOP. New functionality for automated prediction of protein domains, based on Protein Domain Parser.
- Improvements and bug fixes in several modules.

Currently, up to 8 different people are making commits per month. This gives an indication how active Biojava is being developed. The two new modules are based on the work of Ah Fu (Chuan Hock Koh) and Peter Troshin, which happened around this year's Google Summer of Code. Thanks to everybody who made this new release possible!

Google Summer of Code 2011

BioJava is participating again in this year's Google Summer of Code. We are currently accepting student applications. For more info see here Google_Summer_of_Code

BioJava 3.0.1 released

BioJava 3.0.1 was released on Feb 13th 2011 and is available from BioJava:Download.

The 3.0.1 release is mainly a bug fixing release for the recent 3.0 released which provided a major rewrite of the biojava code base. A couple of noteworthy bug fixes:

- core: fixed an issue with sequence index positions, new utility methods for parsing of large fasta files

- structure: Fixed issues with PDB header parsing and more stability with non-standard PDB files. Added new algorithm to automatically infer protein domain boundaries.

- web services: Fixed wrong dependency on old codebase and overall improvements in functionality

- protein modifications: Minor bugfixes

In parallel the biojava-legacy code base has been updated to release version 1.8.1 and it provides a bug fix related to circular locations.

Thanks to all contributors for making this release possible.

Happy Biojava-ing

BioJava 3.0 released

Biojava 3.0 was released on Dec 28th 2010.


BioJava 3.0 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.

Over the last year BioJava has undergone a major re-write. It has been modularized into small, re-usable components and a number of new features have been added. The new approach, modeled after the apache commons, minimizes dependencies and allows for easier contribution of new components.

At the present the main modules are:

biojava3-core: The core module offers the basic tools required for working with biological sequences of various types (DNA, RNA, protein). Besides file parsers for popular file formats it provides efficient data structures for sequence manipulation and serialization.

biojava3-genome: The genome module provides support for reading and writing of gtf, gff2, gff3 file formats

biojava3-alignment: This module provides implementations for pairwise and multiple sequence alignments (MSA). The implementation for MSA provides a flexible and multi-threaded framework that works in linear space and that, as an option, allows the users to define anchors that are used in the build up of the multiple alignment.

biojava3-structure: The 3D protein structure module provides parsers and a data model for working PDB and mmCif files. New features in this release are the implementation of the CE and FATCAT structural alignment algorithms and the support of chemical component definition files, for a chemically and biologically correct representation of modified residues and ligands.

biojava3-protmod: The protein modification module can detect more than 200 protein modifications and crosslinks in 3D protein structures. It comes with an XML file and Java data structures to store information about different types of protein modifications collected from PDB, RESID, and PSI-MOD.

Not every feature of the BioJava 1.X code base was migrated over to BioJava 3.0. A modularized version of the 1.X sources is available as a new "biojava-legacy" project.

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.

the presentation

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.

BioJava News

Call for Organization Admins for OBF?s 2014 Google Summer of Code participation

Update: The deadline for responding has been extended to January 25. The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline puts the mentoring organization applications from Feb 3 to 14. OBF participated on behalf of … Continue reading

BioJava 3.0.4 released

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 … Continue reading
OBF and Google Summer of Code 2011

Google announced today the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for the 2011 Google Summer of Code! Continue reading
Introduction of OpenID logins for OBF wikis

Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new user account creation and adding OpenID logins for the OBF wikis (BioPerl example). User account creation via the old login … Continue reading
OBF Redmine server now available
O|B|F Google Summer of Code Accepted Students

I’m pleased to announce the acceptance of OBF’s 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) – Improvements to BioJava including Implementation of Multiple Sequence Alignment … Continue reading
O|B|F in Google Summer of Code

O|B|F is in Google Summer of Code, student applications due to Google April 9, 2010. Continue reading
Sanger FASTQ format and the Solexa/Illumina variants

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 … Continue reading
Server downtime announcement

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?biojava in anger? translated to French and Japanese

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