The following list of modules for BioJava have been defined and the following people have stepped up to become module leader:
Module: biojava3-core Lead: Scooter Willis
Module: biojava3-structure Lead: Andreas Prlic
Module: biojava3-alignment: Lead: Mark Chapman
Module: biojava3-modfinder: Lead: Jianjiong Gao
Module: biojava3-phylo: Lead: Scooter Willis
Module: biojava3-genome: Lead: Andy Yates
Module: biojava3-ws: Lead: Sylvain Foisy
Module: biojava3-aa-prop: Lead: Chuan Hock Koh
Module: biojava3-protein-disorder: Lead: Peter Troshin
If you are looking for a BioJava related project, consider contributing one of the missing Feature Requests.
There are also a number of algorithms where we would be interested in Java ports.
Legacy BioJava 1.8
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
- 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 secondary structure assignment
- better integration with 3D viewers (Jmol, RCSB viewers)
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
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.