[Biopython-dev] python biocorba <-> ensembl

Brad Chapman chapmanb at arches.uga.edu
Wed Feb 21 14:53:33 EST 2001

Hi Thomas;

> I need to work with the ensembl data (www.ensembl.org) and the only ways
> skipping perl is to implement ensembl calls in python or use
> (as Ewan Birney suggested) a Perl<->CORBA<->Python bridge.

I was following this on the ensembl-dev list, and I think it would be
very cool to have an ensembl-based server that you could get to
through biocorba (or expanded biocorba). Since the bioperl-corba
server is nearly done (thanks to Jason!), it seems like we would only
need to think up an IDL for some of the interfaces, and build this top 
level server. 

I'm ccing this to Jason, who mentioned that he might want to help
write a perl server for ensembl (and I'm holding him to it :-). If he, 
or Ewan could provide this, then I would be happy to do the
biopython-corba nuts and bolts stuff from the python side. Then Thomas 
would get to be the guinea pig to test it...

> ... the question is how should I start with Corba ???
> Is there anything I could use in the biocorba stuff or should I go directly
> for corba+python ??? 

Biocorba is definately your best bet here. All of the lower level
objects (like Sequences, Features, etc) are already accessible through 
biocorba. You would just need the high level layer to connect with

> Any pointers, quick tutorials etc. ???

Of course! Alan Robinson just wrote a very nice tutorial to
getting started writing CORBA clients at:


[Sorry about the wrapping on that URL]
There is a python section to the Tutorial.

This is a big picture kind of introduction to CORBA. There are also
quite a bit of docs on using biocorba from python. They are liked to
from the BiopythonCorba wiki page at:


I'm also willing to help with questions, etc. I'm very happy to see 
biocora utilized, and definately think it is the right way to go
here. Convincing Jason or Ewan to provide a ensembl corba server is 
much easier then writing python wrappers around ensembl internals :-).


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