[Biojava-dev] drafting the release announcement

[Scooter Willis]

Andreas

Looks good.

Scooter

On Dec 28, 2010, at 12:27 PM, Andreas Prlic wrote:

> Thanks Scooter and Jianjiong for your comments, here an updated
> version incorporating your suggestions. The announcement will
> primarily be posted on the biojava mailing lists, but in the past we
> sometimes had re-distribution of the release announcements by other
> news channels. As such I want it to be written similar to a
> press-release.
> 
> 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 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.