[Bioperl-l] contributing? sure!

Jason Stajich jason@chg.mc.duke.edu
Tue, 11 Jul 2000 10:57:43 -0400 (EDT)

On Tue, 11 Jul 2000, Ewan Birney wrote:

>  o There are projects that need deepening -
>     - biocorba access
>     - bioperl-db might be running (? Jason)

[ more than you'd like to know, but while we're putting out wish lists ]

Biocorba needs performance evaluation, memory usage, heavy load testing.
I'd like to see a more robust server built to produce a usable
client/server framework rather just the examples we are providing.

bioperl-db is an effort to provide sequence database access and support
for updateable sequences (and the annotations) outside of the core bioperl
read-only seq db support.

Currently this is being implemented using the Ensembl db structure (with
some additional tables) on a mysql db server.  The ultimate goal for
ensembl-lite (in my mind at least) is a reasonable framework for
small/midsized laboratories to store their genomic data and access to the
analysis pipelines (a lite-r version than the standard ensembl pipeline).  
When the DAS standard is completed we would also like to make an
ensembl-lite a DAS server.

AceDB support as well would be nice to allow users to access data in the
ensembl-lite system transparently if it is in the mysql db, and acedb
file/server, or a remote web db (GenBank, others ... ).  Other ideas or
additions will be welcome. 

I am in the mid stages of the updatableseqdb implementation, and still
designing the rest of the structures.  Suggestions, volunteers, support is
welcome of course.

Jason Stajich
Center for Human Genetics
Duke University Medical Center
(919)684-1806 (office)
(919)684-2275 (fax)