[Bioperl-l] pipeline

[Ewan Birney]

On Mon, 11 Mar 2002, Elia Stupka wrote:

> (Apologies for the cross-post)
> 
> We are going to be working with Jason on getting Trees,Alignments,etc. to
> work more and more in bioperl and bioperl-db. At the same time, this is
> part of our in-house development of synteny stuff in compara, and ideally
> we would like to run all of these with ensembl-pipeline.
> 
> As we rely entirely on bioperl-db for our sequence handling, and as I am
> keen to see more going into bioperl, we are now bound to get a better
> runnable system in bioperl and runnabledb system in bioperl-db.

[snip the rest of the post]



Elia -


I don't mind at all a sort of rewriting/retooling of parts of Ensembl
drifting "into" Bioperl/BioSQL. I think that's both natural and allows
Ensembl to stay focused on being able to turn around big-bad-genomes for
the Ensembl "pro" teams but gives the broader bio* community access to
the technology. 


I was expecting this sort of thing to happen, so I'm not surprised.



What I would like to ensure is that we don't have large overlaps of
development between bioperl and ensembl - eg, if we eneded up having *two*
systems for storing trees that would be a no-no. The key here is
communication between all the people. 



So... lots of email/meetings/coordination.


But as there are a good number of people aware of both projects, I don't
expect much drama.