BioJava 3.0.8 released

 BioJava 3.0.8 was released on March 25th 2014 and is available from

http://biojava.org/wiki/BioJava:Download as well as from the

BioJava maven repository at http://www.biojava.org/download/maven/

This release would not have been possible without contributions from

13 developers, thanks to all for their support!

BioJava 3.0.8 includes a lot of new features as well as numerous bug fixes and improvements.

New Features:

•  new Genbank writer
•  new parser for Karyotype file from UCSC
•  new parser for Gene locations from UCSC 
•  new parser for Gene names file from genenames.org
•  new module for Cox regression code for survival analysis
•  new calculation of accessible surface area (ASA)
•  new module for parsing .OBO files (ontologies)
•  improved representation of SCOP and Berkeley-SCOP classifications

 

For a detailed comparison see here:

https://github.com/biojava/biojava/compare/biojava-3.0.7...biojava-3.0.8

For the next release we are planning some refactoring and removal of code that has been deprecated for a long time. As such the next release will be named 3.1.0.

About BioJava:

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.

Happy BioJava-ing,

Andreas

biojava-structure now supports Chemical Component Dictionary

I have updated the BioJava structure data model to support the PDB
chemical component dictionary. This has the benefit that now

* Chemically modified amino acids can be detected (and treated as
amino acids, rather than Hetatom groups)
* It is possible to get a component type for each Group, which allows
to identify ligands.

As a consequence the nr. of amino acids in a chain can change compared
to the previous data representation. As such the loading of chem.
comps is set to "false" by default. It can be configure by the
"loadChemCompInfo" flag in the PDB/mmCIF file parsers.

PDB ID 1A4W - Thrombin with Thiazole-containing Inhibitors. Image source: RCSB PDB

An example where this representation makes a difference is PDB ID 1A4W. This structure contains several Ligands and a chemically modified residue. Without the help of the Chemical Component Dictionary it would have been difficult to correctly represent this protein.

You can get the code either from BioJava SVN, or from the (still slightly experimental) Maven repository at http://www.biojava.org/download/maven/ .

An easy way to set up a web site (using Java, Maven and Eclipse)

Download the following open source software:

* Tomcat 6 from http://tomcat.apache.org/download-60.cgi
unpack it in a local directory. (I got the Core tar.gz one)

* Eclipse (the JEE edition) from http://www.eclipse.org/downloads/
launch Eclipse


In Eclipse:

* Install the Maven (m2eclipse) plugin for eclipse by adding

http://m2eclipse.sonatype.org/update/

as a new site under Help->Install New Software-> Add

Select the the checkboxes of the modules you want to install.


Create a new Eclipse project

* Select File-> New -> Other -> Maven Project

leave project name and location to the default values



as a project Archetype select maven-archetype-webapp



as a group ID select the name of your organisation e.g. org.biojava

Artifact ID is the name of your module. E.g.: myweb (this will also be in your servlet URL)




This will create the following servlet in your workspace.



Deploy the project on Tomcat

* Add a new Tomcat 6 server : Select File-> New -> Other -> Server

* select Apache-> Tomcat 6



* point it to the location at which you upacked Tomcat


* add your servlet to it and press Finish


* Start your server buy either clicking the green button, or right click on your servlet project and say Run As -> Run on Server

* Tomcat will start and the servlet is running


Add new jsp pages and start the development of your servlet!

Finally: If you want to give the servlet to your sysadmin to release on a production site, just do a Right click on the project and do Run As -> Maven package . This will create a myweb.war in the target subdirectory of your project that can be deployed in stand alone tomcat instances outside of eclipse.