[Biocorba-l] Biocorba IDL
Alan Robinson
alan@ebi.ac.uk
Fri, 3 Nov 2000 17:14:32 +0000 (GMT Standard Time)
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Hi,
On Thu, 19 Oct 2000, Alan Robinson wrote:
> I'm writing a Biocorba server currently (planned to be released next
> week), and whilst working with the Biocorba IDL I've come across the
> following issues:
OK - A little later than expected and not entirely finished, but I'd like
to put forward a prototype biocorba server.
The server which we're currently testing is a biocorba wrapper around a
replication of the complete production EMBL nucleotide sequence database
via our own EMBL CORBA server (see http://corba.ebi.ac.uk/).
So through the EBI's biocorba server, you'll have access to all 9,000,000+
sequences in EBML-Bank (aka GenBank).
Caveat emptor - The Biocorba server is temporarily working off an ancient
SGI. But you can find a *TEMPORARY* IOR at
http://industry.ebi.ac.uk/~alan/IOR/
called
org.Biocorba.Seqcore.BioEnvPOAImpl-Server.ior
I've attached a little perl client that connects to the server and pulls
over data from it. You'll also need the BioCorba.idl file, which I've
attached for convenience, as well as the ORBit orb and perl binding (you
can find these via CPAN if necessary).
For those of you who are Java-enabled, I've included a Java client too.
(Personally, I'd recommend ORBacus as a good free Java ORB).
You can query the EMBL SeqDB object by accession number or entry ID.
Not all methods are implemented for the EMBL SeqDB object - In particular,
you cannot get a PrimarySeqIterator, or the accession numbers of all Seq's
in the EMBL SeqDB.
At the moment, we're working on a proposal for a next version of the
BioCorba IDL and an implementation (I'll try and post next week).
We're also itching to get the bioperl-gui working with biocorba. As an
alternative, we may implement the relevant bioperl interfaces (Bio::SeqI,
etc) as an IDL interface.
Obviously any feedback and bug reports would be most appreciated.
cheers,
al
--
============================================================
Alan J. Robinson, D.Phil. Tel:+44-(0)1223 494444
European Bioinformatics Institute Fax:+44-(0)1223 494468
EMBL Outstation - Hinxton Email: alan@ebi.ac.uk
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD, UK http://industry.ebi.ac.uk/~alan/
============================================================
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