[Biojava-dev] BioJava code freeze, modularization and action items for sub modules

[Andreas Prlic]

Hi,

In order to push the modularization and migration to Maven, I would like to
declare a code freeze on the current developmental trunk. Please commit all
new changes by

Thursday 27th of August 23:00 GMT.

In the week after I would like to refactor the code base and commit the
initial set of modules to a new developmental trunk.  All future development
will happen on that new trunk.

You will be able to follow the ongoing status of this at

http://biojava.org/wiki/BioJava:MavenMigration


Once the modules are in place it is a good moment to hand over the
leadership of the sub-modules to the new module-project leaders. It will be
up to the module-lead to take the modules into the direction that he/she
feels important. I would like to take this opportunity to suggest a couple
of people as module-leaders and propose some action items for the modules.
Feel free to comment or make additional suggestions...

Here a list of modules / action items and the people that I would propose to
become module leaders:

Module: biojava-core Lead: Andreas Prlic
 - break the new modules out of core
 - 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

Module: biojava-alignment Lead: Andreas Draeger
 - allow better access to underlying dynamic programming data structures
 - allow more customizable display of pairwise alignments (HTML/plain text,
etc)

Module : biojava-blast Lead: still looking for a leader
 - 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


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-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

Module: biojava-sequencing Lead: ???
  - support FastQ files
 - support parsing of output for various new sequencing machines

This is only an initial set of modules and I think it is safe to say that
more modules will be added after more discussions (and people volunteering
to contribute).

Andreas