Thanks, Mark. Guess we should start collecting all this info on a wiki page. I started to edit http://biojava.org/wiki/BioJava:Modules
module leaders: feel free to edit the plans for your module... Andreas On Thu, Aug 27, 2009 at 10:37 PM, Mark Schreiber<[email protected]> wrote: - Show quoted text - On Thu, Aug 27, 2009 at 10:37 PM, Mark Schreiber<[email protected]> wrote: > I'm happy to volunteer code for: > > BLASTXML parser as long as I can change the ssbind APIs (other parsers could > go into a legacy module??). Actually I would prefer to completely decouple > from the sequence/ feature module as many people would like a blast parser > without the rest of biojava thrown in. > BioSQL/ JPA bindings. I have already generated JPA compliant entity beans > for mapping to BioSQL as well as JPA handler code that makes sure > modifications presist properly. Currently the object model very closely > follows the BioSQL table structure. Also the current beans are what people > call Anaemic beans in that they hold data and provide getters and setters > but no biological behaivour. I can easily provide bio-smarts to the beans > but it might be better to hold off until there is a module that contains > sequence/feature interfaces which the beans could implement. > Happy to provide code for an enterprise module if there is sufficient > interest. 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. > > - Mark > > > On Fri, Aug 28, 2009 at 1:30 AM, Andreas Prlic <[email protected]> wrote: >> >> Great, thanks for "volunteering", Michael. >> >> To add another Module: >> >> biojava-das : Lead: Jonathan Warren >> probably deprecate the old DAS code in BJ and replace it with >> the up to date Dasobert library >> >> Thanks to Jonathan for volunteering as well. >> >> Andreas >> >> >> >> >> On Thu, Aug 27, 2009 at 10:01 AM, Michael Heuer<[email protected]> wrote: >> > Andreas Prlic wrote: >> > >> >> Here a list of modules / action items and the people that I would >> >> propose to >> >> become module leaders: >> >> ... >> >> >> >> Module: biojava-sequencing Lead: Michael Heuer >> >> - support FastQ files >> >> - support parsing of output for various new sequencing machines >> > >> > I have volunteered on the open-bio mailing list to implement FASTQ >> > support. A nice collection of test data is being created in >> > collaboration >> > with the other open-bio projects. If anyone has interest in a >> > particular >> > data set, please let me know, as I will also need data for performance >> > tuning. >> > >> > michael >> > >> > _______________________________________________ >> > biojava-dev mailing list >> > [email protected] >> > http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
