Current events
BioJava 4.0.0 released
BioJava 4.0.0 has been released and is available using Maven from Maven Central as well as through manual download.
This release contains over 500 commits from 17 authors:
@andreasprlic @benjamintboyle @christiam @dmyersturnbull @Elinow @emckee2006 @jgrzebyta @josemduarte @kevinwu1 @pibizza @heuermh @paolopavan @parit @pwrose @sbliven @sroughley @willishf
BioJava 4.0.0 is a major release, with many new features as well as core API changes. In accordance with semantic versioning nomenclature, the jump to 4.x.x indicates that existing applications may need to be modified (e.g. due to the removal of deprecated methods). In most cases there should be a clearly documented replacement method. See below for details on how to upgrade.
New Features:
- General
- Consistent error logging. SLF4J is used for logging and provides adaptors for all major logging implementations. (many contributors, including @benjamintboyle and @josemduarte)
- Improved handling of exceptions (@dmyersturnbull)
- Removed deprecated methods
- Expanded the BioJava tutorial (@andreasprlic, @josemduarte, and @sbliven)
- Updated dependencies where applicable
- Available on Maven Central (@andreasprlic and @heuermh)
- biojava3-core
- Improved Genbank parser, including support for feature records, qualifiers, and nested locations. (@paolopavan and @jgrzebyta)
- biojava3-structure
- Better support for crystallographic information, including crystallographic operators, unit cells, and protein-protein interfaces. (@josemduarte)
- Better organization of downloaded structure files (set using the PDB_DIR and PDB_CACHE_DIR environmental variables) (@sbliven)
- Better command-line tools for structure alignment (@sbliven)
- New algorithm for symmetry detection in biological assemblies (@pwrose)
- New algorithm for fast contact calculation, both intra-chain and inter-chain (@josemduarte)
- Support for Accessible Surface Area (ASA) calculation through and implementation of the Shrake & Rupley algorithm, both single-thread and parallel (memory permitting) (@josemduarte)
- Support for large structures (memory permitting) and multi-character chain IDs.
- Default to mmCIF file format, as recommended by the wwPDB
This version is compatible with Java 6, 7, and 8.
Upgrading Since we renamed all package names to be consistent across the whole project, there will be import errors when upgrading to this version. These can automatically get resolved by IDEs such as Eclipse or IntelliJ by selecting the Optimize Import menu item.
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,
BioJava 3.1.0 released
BioJava 3.1.0 was released on August 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/
While most development is going towards the upcoming 4.0.0 release, this release provides bug fixes and a few new features:
- CE-CP version 1.4, with additional parameters
- Update to SCOPe 2.04
- Improvements in FASTQ parsing
- Fix bugs in PDB parsing
- Minor fixes in structure alignments
For a detailed comparison see here: https://github.com/biojava/biojava/compare/biojava-3.0.8...biojava-3.1.0
This version is compatible with Java 6 and 7. If you're using Java 8, please use the latest snapshot build. Snapshots are now available from Maven central just by setting your pom.xml file to version '4.0.0-SNAPSHOT'!
Thanks to the contributors who submitted code to this release–heuermh, Elinow, Siarhei, sbliven and andreasprlic–and to those who contributed to the 4.0.0 branch!
BioJava 3.0.8 released
BioJava 3.0.8 was released on March 25th 2014 and is available from BioJava:Download as well as from the BioJava maven repository at http://www.biojava.org/download/maven/
This release 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
This release would not have been possible without contributions from 13 developers, thanks to all for their support!
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,
BioJava 3.0.7 released
BioJava 3.0.7 was released on September 23rd and is available from BioJava:Download as well as from the BioJava maven repository at http://www.biojava.org/download/maven/ .
new features:
- added a basic genbank parser - fixed a problem when translating codons with N - now can infer bonds in protein structures - added support to parse mmcif records for organism and expression system - many small bug fixes and improvements
BioJava Legacy 1.8.4 released
BioJava Legacy 1.8.4 was released on August 27th 2013 and is available from BioJava:Download_1.8.4 as well as from the BioJava maven repository at http://www.biojava.org/download/maven/ .
New Features:
- We moved our development to Github - Minor improvements to the sequencing module - Build/release fixes
BioJava 3.0.6 released
BioJava 3.0.6 was released on July 15th 2013 and is available from BioJava:Download as well as from the BioJava maven repository at http://www.biojava.org/download/maven/ .
New Features:
- We moved our development to Github. - many bug fixes and minor improvements
BioJava moves to Github
As of April 3, 2013, Github is the primary repository for BioJava. See SVN to GIT Migration for more info.
BioJava 3.0.5 released
BioJava 3.0.5 was released on Nov 30th 2012 and is available from BioJava:Download as well as from the BioJava maven repository at http://www.biojava.org/download/maven/ .
New Features:
- New parser for CATH classification - New parser for Stockholm file format - Significantly improved representation of biological assemblies of protein structures. Now can re-create biological assembly from asymmetric unit - Several bug fixes.
BioJava 2012 paper published
The latest BioJava paper describing the version 3 series has been published and is now available online.
Thanks to all developers for their contributions, it would not have been possible without them!
[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 3.0.4 released
BioJava 3.0.4 was released on May 21st 2012 and is available from 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) .
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.
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.
