[Biojava-dev] drafting the release announcement

[Scooter Willis]

Andreas

Do you think you should add something about the legacy Biojava code and its status? 

If this is for the biojava dev list then probably don't need details. If for a general audience then may need to discuss that not all features of Biojava were migrated. With the new approach(modeled after apache commons) it minimizes the complexities of contributing new components. We should encourage developers to get involved with existing components and to add new ones.

Scooter


On Dec 28, 2010, at 7:50 AM, Andreas Prlic wrote:

> Hi,
> 
> I am about to trigger the BioJava 3.0 release.   Does the draft for
> the release announcement below cover all new aspects?
> 
> Andreas
> 
> BioJava 3.0 has been released and is available using Maven from
> http://biojava.org/download/maven/
> 
> 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 majore re-write. It has
> been modularized into small, re-usable components and a number of new
> features have been added. 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 their manipulations 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 datamodel 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 Posttranslational Modification module can detect
> three different types of protein modifications in protein structures.
> It comes with an XML file & Java data structures to store information
> about different types of protein modifications, and contains entries
> from RESID, PDBCC and PSI-MOD.