From BioJava

BioJava Modules

The following list of modules for BioJava have been defined and the following people have stepped up to become module leader:

Module: biojava-core Lead: Andreas Prlic

- bring up to modern Java standards, use Generics
- declare old/unused code obsolete
- don;t break backwards compatibility

Module: biojava-sequence Lead: Richard Holland

- Bring in Richard's new code that he started to develop on the biojava-3 branch.
- provide a more scaleable and efficient basis for dealing with large sequence files
- consider implementation based on ParallelArray from JSR166 (extra166y package, see http://gee.cs.oswego.edu/dl/concurrency-interest/)
- consider implementation that supports MapReduce as in Apache Hadoop (http://hadoop.apache.org/)

Module: biojava-alignment Lead: Andreas Dräger

- refactoring of underlying data structures
- allow better access to underlying dynamic programming data structures
- allow more customizable display of pairwise alignments (HTML/plain text, etc)

Module : biojava-blast Lead: Mark Schreiber

- provide access to all details of the blast output
- add support for RPS blast

Module: biojava-phylo Lead: Scooter Willis

- provide improved NJtree /Jalview

Module: biojava-biosql Lead: Richard Holland

- merge the new biojava-sequence module with the current biojava-biosql code 
- Mark Schreiber wants to work on BioSQL/ JPA bindings

Module: biojava-das : Lead: Jonathan Warren

- probably deprecate the old DAS code in BJ and replace it with
= the up to date Dasobert library
-update dasobert code to 1.6 and make smaller
-add further support for getting new information contained in the registry (validation, on the fly validation, sources by types and cvId).

Module: biojava-structure Lead: Andreas Prlic

- add support for SCOP file parsing
- add support for easy access of domains (in terms of coordinates)
- add secondary structure assignment
- improve structure alignments
- better integration with 3D viewers (Jmol, RCSB viewers)

Module: biojava-sequencing Lead: Michael Heuer

- merge FASTQ support from 1.7.1 branch to trunk
- provide facade for Fastq --> Biojava sequence with quality scores
- review FASTQ IO interfaces, compare design with Richard's biojava3

Module: biojava-web services:

- The details seem still to be under discussion and perhaps we need multiple modules here?
- also what about REST vs. SOAP? To be discussed. People who expressed interest are:
- Niall Haslam,Scooter Willis, Sylvain Foisy

Module?: biojava-ws-blast Module?: biojava-ws-biolit

Proposed Module: biojava-j2ee Lead: Mark Schreiber

- This would probably take the form of SessionBeans and WebServices that can be deployed to Glassfish/ JBoss etc to provide biological services  for people who want to make client server or SOA apps.