[Bioperl-l] want to bring tools together to help small labs

[Jason Eric Stajich]

We have a bioperl-db that Ewan started which effectively represent a
genbank db in mysql and allow easy mapping of sequences in the DB to in
memory Bio::Seq objects.  Not clear how much different the schema is from
Ian's myGenBank but this definitely geared towards intefacing nicely with
the bioperl Bio::SeqI interface.  It is rumoured to also be used as a
local caching server for BioCORBA sequence requests at EBI for fast
relation DB access to sequences.

The GenQuire folks (Mark Wilkinson, David Block)
also have a db for curation of data and a perl/Tk interface - parts of
this are distributed in bioperl-gui.  They may be changing their schema to
play with bioperl-db more directly - not sure about that.  Rumor has it
they are moving Genquire to full open-source mode so that others can
contribute.

See the news item about bioperl-db:
http://bioperl.org/pipermail/bioperl-l/2001-April/005465.html

cvs module name is bioperl-db
see info at
http://cvs.bioperl.org on how to checkout a local copy.

This also some beginning work in there for map databases but is currently
on hold until I find some more time or get more contributors.

-jason

On Fri, 2 Nov 2001, Fernan Aguero wrote:

> Dear T.D.and bioperlers:
>
> Have you had any positive responses and/or suggestions? are there
> other people interested in this?
>
> Some time ago we needed the same thing and looked into how ensembl was
> doing things since we also wanted to use a relational database backend
> to store info and then generate the web pages on the fly through CGI
> scripts. For us it was too complex and also had a bias toward higher
> eukaryotes, which we did not needed (we work with bacteria and
> protozoa).
> In the end we developed our own db schema, scripts and so on ... but
> as a first attempt at it I know it is far from being _the_right_thing_
> First of all it is too much customized to our own projects and way of
> working.
>
> So we now would like to have something more generic, more modularized
> and ... simple. So if we agree on the goals (I would also like to add
> EST clustering to the list) perhaps we could join our effort.
>
> I haven't looked into bioperl lately, but I thought there was a
> bioperl-db or something like this ... I don't seem to find it right
> now. I had the idea (perhaps misguided) that it was a generic db
> schema and modules to store sequence info and annotation, am i right?
>
> If this is of no interest to the list we can discuss it in private.
>
> Regards,
>
> Fernan
>
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu