[DAS] pathways

[Kulp, David]

I haven't looked at AGAVE for a while, but my biggest concern is that it
does not have a good implementation of alignments/assemblies.  Alignments,
for example, were stored as BLAST snippets, if I remember correctly.

My gut feeling is that ALL of this boils down to a clean representation of
alignments.  This becomes a key issue when dealing with genome assemblies
and versioning.  One can imagine, for example, an EST aligned to a BAC, the
BAC assembled to a contig for version A, and that contig aligned to a new
genomic assembly contig for version B.  If alignments are fundamental, then
transfering annotations becomes much more tractable.

Will DoubleTwist's bankruptcy impact this decision?  The agave web site is
down and DoubleTwist owns the DTD and has, presumably, the right to modify
the licensing terms at any time.

Besides these concerns, AGAVE was pretty nice.

-d

> -----Original Message-----
> From: Lincoln Stein [mailto:lstein@cshl.org]
> Sent: Wednesday, April 17, 2002 7:18 AM
> To: Ewan Birney; Tony Cox
> Cc: Matthew Pocock; das
> Subject: Re: [DAS] pathways
> 
> 
> On Wednesday 17 April 2002 06:54, Ewan Birney wrote:
> > On Wed, 17 Apr 2002, Tony Cox wrote:
> > > On Wed, 17 Apr 2002, Matthew Pocock wrote:
> > >
> > > +>Hi all,
> > > +>
> > > +>Is there any general interest in a distributed open and 
> extensible
> > > +>web-service architecture for publishing and integrating 
> pathways and
> > > +>annotations of pathway elements or sub-networks?
> > >
> > > hmmm... I'd love to see DAS2 working first ;)
> >
> > Ditto.
> 
> Me too.
> 
> Since most of the hang-up is over the features 
> representation, and since 
> Brian, Matt and Thomas have all expressed enthusiasm over 
> AGAVE, I vote that 
> we adopt AGAVE as the response to the DAS/2 features request 
> and move on to 
> more interesting issues.  Any nay-sayers?
> 
> Lincoln
> 
> 
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