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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
