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

[Mark Schreiber]

I'm happy to volunteer code for:


   1. 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.
   2. 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.
   3. 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 <andreas at sdsc.edu> 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<heuermh at acm.org> 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
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
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