[Biojava-l] BioJava discussion board

[Schreiber, Mark]

Hi -

I have played with the biojava Agave support and it's a bit flaky right
now, round tripping gets you back to a place which doesn't look like
kansas anymore (if I may mix my metaphores).

As long as we can sort out the wrinkles I think that standardising on an
XML object could be the way to go. It also lends itself to having a
package of data blobs that use JAXB to bind to the XML, there are
utilities to automagically generate these from a DTD.

- Mark


> -----Original Message-----
> From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] 
> Sent: Thursday, 29 August 2002 8:48 a.m.
> To: Thomas Down
> Cc: Brian Gilman; Patrick McConnell; biojava-l@biojava.org
> Subject: Re: [Biojava-l] BioJava discussion board
> 
> 
> Does agave allow you to push annotations arround without the 
> sequence? 
> In a web service environment we may not want to push the dna 
> for chrom I 
> arround even though we may want to know all features within a 
> region of 
> it. I am format agnostic. The important things are that:
> 
> a) any format can potentialy be easily made and consumed by lots of 
> services/clients (including our own)
> 
> b) the web services are sliced at the right level of granularity
> 
> Mmm.
> 
> Thomas Down wrote:
> > On Wed, Aug 28, 2002 at 09:35:59AM -0400, Brian Gilman wrote:
> > 
> >>I agree with Patrick on that one. Perhaps Agave could be 
> used as the 
> >>serialzation layer here?? It would be a little bit of work to get 
> >>everything munged into Agave or BSML but think about the 
> benefits for 
> >>we poor middleware guys!
> > 
> > 
> > Yep, I'm with you on this, too.  I'm not actually that 
> bothered about 
> > exactly /which/ schema gets used -- Agave seems about as sane as 
> > anything right now (and we have some support for it already in 
> > BioJava, which makes life easier for us :-).
> > 
> >       Thomas.
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org 
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
> 
> 
> -- 
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> http://www.biojava.co.uk
> 
> 
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