[Biojava-l] Dazzle server update

[Lincoln Stein]

Outstanding, on both the client and dazzle fronts!

Lincoln

Thomas Down writes:
 > The latest development version of Dazzle, my DAS server toolkit, is now
 > available via CVS from the BioJava repository.  Details of
 > how to access this can be found on http://cvs.biojava.org/.
 > The module name is "dazzle".
 > 
 > Dazzle is a Java servlet which uses to BioJava core APIs
 > for handling sequence data and tables of features.
 > The idea is to provide a simple framework for handling DAS
 > requests and generating the basic documents, which can be
 > parameterized for specific purposes by plugging in one or
 > more DASDataSource objects.  These allow the same servlet
 > to work well as either a reference or an annotation server
 > on the DAS network.  I've got a couple of plans in mind for
 > Dazzle:
 > 
 >   - Combine with the experimental biojava-ensembl bridge code
 >     to serve human genome data directly out of the Ensembl
 >     project's SQL database.  This is a good testcase for Dazzle
 >     as a practical, scalable (!) server, as well as providing
 >     a sensible reference point for other people wanting to offer
 >     human annotation.  The bridge code is very close to a position
 >     where I could serve sequence data (a little bit more work is
 >     still needed to get genes and features working, though).
 > 
 >   - Package dazzle with a standalone servlet container (Tomcat?
 >     Interalia picoServer? something else?) and a simple admin
 >     tool to give a `10 minute' DAS server installation.  This
 >     should allow you to drop in some GFF/Game/whatever files and
 >     start serving annotations straight away).  
 > 
 > There are a few changes since the 0.04 tarball I put out a 
 > while back:
 > 
 >   - No longer needs to build from the same source tree as
 >     a DAS client -- I use the standard BioJava client code
 >     instead.
 > 
 >   - Some of the scalability bottlenecks fixed (but still more
 >     to go -- startup time for annotation servers is rather slower
 >     that I'd hope).
 > 
 >   - Tidied up the output -- should be able to generate 100%
 >     compliant DAS/0.98 documents.
 > 
 > If anyone is in a hurry to try it, the instructions for 0.04 should
 > still work.  Otherwise, in the next few days I'm hoping to make the
 > following changes:
 > 
 >   - Stabilise the DASDataSource interface
 > 
 >   - Migrate to servlets 2.2 (it currently builds against 2.1,
 >     but I don't know of any production quality 2.1 containers)
 > 
 >   - Improve lazy data source instantiation.
 > 
 >   - Write new installation documents.
 > 
 > I'll make a `proper' release once these changes are made.
 > 
 > Thomas.
 > -- 
 > ``If I was going to carry a large axe on my back to a diplomatic
 > function I think I'd want it glittery too.''
 >            -- Terry Pratchett

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY

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