[Biojava-l] Temporary DAS server

[David Huen]

I've been exploring the problems and limits of Ragbag-based DAS service
and have tried to see the feasibility of serving real-life data thru'
Dazzle/RagbagDataSource and getting some source to work on a viewer.

I've finally managed to get a DAS server based on Dazzle
serving the Berkeley Drosophila Genome Project GAME-XML files with my
RagbagDataSource object.  That's roughly 120 Mbases of sequence +
annotations I think.  The shebang is running on a small machine: Cyrix
PR333 (250 Mhz real clock rate) with 256MB RAM.  Don't expect
blistering performance!  Since the system uses lazy instantiation,
there will be a brief pause whenever a component boundary is crossed
(roughly every 300 kb) The features constitute a subset of the full
annotations but will be extended as I improve GAME support in my browser.

The server will be up and down over the next few weeks as I work on
improving Ragbag for use as a DataSource but it may prove useful to some
as another test DAS server dataset.

I've prepared a standalone viewer using some of the newer Renderer classes
in biojava in it too. (I hope I assembled it right!).  It will be rather
slow because it's trying to do too much, like compute stops and frames for
the six frame renderers from only transcript data (no CDS data).

You can wget that from:-
http://www.huen.org.uk/david/viewer.jar

for a short time but go easy on it - I don't want my ISP going
ballistic on me!

Regards,
David Huen, Dept. of Genetics, Univ. of Cambridge