[Biojava-l] Dazzle server update

[Thomas Down]

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