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

[Andreas Prlic]

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<markjschreiber at gmail.com> wrote:
- Show quoted text -

On Thu, Aug 27, 2009 at 10:37 PM, Mark
Schreiber<markjschreiber at gmail.com> 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 <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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>