[Biojava-l] biojava 1.5 beta release

mark.schreiber at novartis.com mark.schreiber at novartis.com
Fri Sep 8 05:58:39 UTC 2006

Dear All -

I have prepared a beta distribution of the much awaited biojava 1.5. The 
source, binaries and docs for the release can be obtained from the biojava 
site at http://biojava.org/wiki/BioJava:Download

The API docs are also available on line at 

There are significant new features in this release:

* biojavax, the biojavax packages are extensions to the basic biojava. 
They give access to more detailed objects with better functionality. Most 
useful to the average user will be the new file parsers (see 
RichSequence.IOTools) and the RichSequence object. See the biojavax docs 
for more detail (http://biojava.org/wiki/BioJava:BioJavaXDocs).

* Hibernate interaction with BioSQL. The prefered method of interaction 
with BioSQL is now via Hibernate. RichSequence and it's associated objects 
have hibernate mappings to biosql databases. This provides a number of the 
benefits of Hibernates ORM to biojava, especially control over 
transactions and the removal of JDBC code. See 
http://biojava.org/wiki/BioJava:BioJavaXDocs#BioSQL_and_Hibernate. for 

* Genetic Algorithms. A very flexible genetic algorithm library is 
available in the biojavax packages. Simple examples are at 
http://biojava.org/wiki/BioJava:BioJavaXDocs#Genetic_Algorithms. but much 
more powerful things are possible.

* Several new features are available in the Structure package that allow 
manipulation of 3D structure files and objects.

* Non HMM Implementations of the NW and SW alignment algorithms are now 
available in the alignment package.

* A new package for handling external processes 

* Dozens of bug fixes.

Please take it out for a spin this weekend and let us know how it works. 
You will probably find it more reliable than biojava-1.4 even though this 
is technically a beta.

Many thanks to all the volunteers who have contributed to biojava!

Best regards,

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670

phone +65 6722 2973
fax  +65 6722 2910

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