[Biojava-l] Re: Experimental DAS 1.900 implementation

[Jason Stajich]

For clarification.

cvs.bio{*}.org is a replication of bio{*}.org not the same machine.  We
rsync the cvs repositories on cvs.bio{*} from bio{*} machine every 2
hours.

So:
cvs.biodas.org is where anonymous cvs will live, devs who need write
access to the das cvs repository will need accounts on the biodas.org,
those just checking out anonymous versions can obtain via cvs.biodas.org
or through webcvs for browsing.  see http://cvs.bioperl.org.

(Chris can you make sure Lincoln's new biodas repositories
 are added to the rsync list when you setup webcvs)

* = (perl|java|python|corba|xml|das) 

On Tue, 12 Jun 2001, Lincoln Stein wrote:

> Hi Thomas, et al.,
> 
> I've moved the biodas repository to cvs.biodas.org (physically the
> same machine as biojava.org, I think).  Shall we move the CVS
> repository there and integrate the biodas.org and biojava.org/das web
> pages? (I'll do the stitching together).
> 
> Lincoln
> 
> Thomas Down writes:
>  > Hi...
>  > 
>  > I've started working on an experimental Java implementation of
>  > the DAS 1.900 proposal, so that we've got something to play
>  > with as the specification develops.  At the moment there's
>  > just a Sequence service (vaguely equivalent to refererence
>  > servers in DAS1).  I've got most of the pieces of a Features
>  > service, and should be able to check that in in the next day
>  > or so.
>  > 
>  > For anyone who's interested in tracking development, there's
>  > code in the BioJava CVS repository (http://cvs.biojava.org/
>  > for more info).  Checkout the module `xdas'.
>  > 
>  > What you get:
>  > 
>  >   - Prototype DAS sequence service
>  > 
>  >   - The SOAP toolkit it relies on.
>  > 
>  >   - An obligatory stock-quote demo ;)
>  > 
>  > To preempt the inevitable question, yes I have looked at other
>  > SOAP toolkits (especially the IBM/Apache one).  While they're good
>  > a lot of the time, they tend to use DOM to represent the SOAP messages
>  > in-memory.  I know from past experience that this really isn't a good
>  > idea where DAS is concerned -- sometimes you want to shift quite
>  > serious amounts of data around (especially feature-tables), and I've
>  > seen OutOfMemoryErrors (as well as poor performance) when the BioJava
>  > DAS client was using a DOM based solution.
>  > 
>  > The new SOAP toolkit is based on S[t]AX event-based XML parsing,
>  > so that should help scalability.
>  > 
>  > 
>  > I'd be interested to hear any comments about this code...
>  > 
>  > 
>  >    Thomas.
> 
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein@cshl.org			                  Cold Spring Harbor, NY
> 
> NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS. 
> PLEASE WRITE FOR DETAILS.
> ========================================================================
> 

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/