[Biojava-dev] drafting the release announcement

[Jianjiong Gao]

Hi Andreas,

I would change the description a little bit for the protmod module as follows:

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

Thanks,
-JJ

On Tue, Dec 28, 2010 at 6:50 AM, Andreas Prlic <andreas at sdsc.edu> 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.
>