[Biojava-l] Dazzle server update
Mon, 20 Nov 2000 11:28:18 -0500 (EST)
Outstanding, on both the client and dazzle fronts!
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
> - 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
> - 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.
> ``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
Lincoln D. Stein Cold Spring Harbor Laboratory
firstname.lastname@example.org Cold Spring Harbor, NY
NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS.
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