Egon Willighagen

Some time ago I blogged about the [ChildResourceCreator extension point
in
Bioclipse](http://chem-bla-ics.blogspot.com/2006/08/bioclipse-gets-new-extension-point.html)
and hinted as using that for [PDB files](http://www.rcsb.org/pdb/).
which contain 3D molecular models, sequences and bibliographic
information. Using the new extension point,
[Bioclipse](http://www.bioclipse.net/) now treats PDB files as complex
documents, creating child resources for the 3D molecular model (using
the [CDK](http://cdk.sf.net/) plugin), and a sequence resource (using
the [BioJava](http://www.biojava.org/) plugin).

![](/assets/images/bioclipseBioJavaSupport.png)

#### References


Some time ago I blogged about the ChildResourceCreator extension point in Bioclipse and hinted as using that for PDB files. which contain 3D molecular models, sequences and bibliographic information.

Complex PDB documents using the Bioclipse ChildResourceCreator

[Martin Szugat
reported](http://www.bioservices.net/2006/09/biojava-15-beta-released.html)
that a beta for [BioJava 1.5](http://biojava.org/wiki/BioJava:Download)
has been released. New features include: a new
[biojavax](http://www.biojava.org/docs/api15b/index.html) package with
extension on the basic functionlity, such as the
`RichSequence.IOTools`{.language-plaintext .highlighter-rouge} and the
`RichSequence`{.language-plaintext .highlighter-rouge} object; a
[genetic algorithm
library](http://biojava.org/wiki/BioJava:BioJavaXDocs#Genetic_Algorithms);
features that allow manipulation of 3D structure files and objects; and
non-HMM implementations of the NW and SW alignment algorithms. The
announcement also mentions a new package for handling external processes
(org.biojava.utils.process); I am wondering what that is about. I will
upload this beta to Bioclipse
[trunk/bc_biojava/](http://svn.sourceforge.net/viewvc/bioclipse/trunk/bc_biojava/)
shortly, so that we can play with it.

#### References


Martin Szugat reported that a beta for BioJava 1.5 has been released. New features include: a new biojavax package with extension on the basic functionlity, such as the RichSequence.IOTools and the RichSequence object; a genetic algorithm library; features that allow manipulation of 3D structure files and objects; and non-HMM implementations of the NW and SW alignment algorithms.

Messaggi di Rogue Scholar

Complex PDB documents using the Bioclipse ChildResourceCreator

BioJava 1.5 beta released