[Bioperl-l] contributing? sure!
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.
Center for Human Genetics
Duke University Medical Center