[DAS2] xml and compact formats

Lincoln Stein lstein at cshl.edu
Thu May 19 16:44:09 UTC 2005

I agree with Gregg on this. There are, for instance, several compact versions 
of XML that use a binary encoding for each tag and attribute.


On Thursday 19 May 2005 10:47 am, Helt,Gregg wrote:
> For the DAS/2 query for features, I think the ability to support
> alternative response formats is critical.  Yes, this is mainly because
> of performance issues -- time to generate the XML on the server, time to
> deliver it over the network, time to parse it and memory footprint on
> the client side.
> Standard compression of the XML format is certainly possible, and unless
> we explicitly forbid it in the spec I see no reason why this can't be
> declared via the standard Accept-Encoding/Content-Encoding HTTP headers.
> But consider if network bandwidth is not the bottleneck (for example
> within an intranet or between sites connected to the Internet2
> backbone).  Compressing with gzip etc. will actually slow things down,
> requiring compression on the server and decompression on the client, and
> not speeding up actual client parsing at all.  From experience I can
> tell you that the decompression cost on the client can be significant.
> Furthermore, more specific binary formats can be much smaller than
> compressed das2feature XML.  For an extreme example, with an optimized
> format my client can parse in ~ 1 million SNP annotations per second.
> And yes, sometimes I need to do that.
> However, although I think the ability to _support_ alternative feature
> formats is critical, I don't think we should be declaring a set of
> alternative feature formats in the specification.  We definitely need to
> have the ability for a server to generate and the client to accept
> annotation formats that the spec itself knows nothing about.  All that
> is needed is a way for the server to indicate which formats it provides,
> and the client to choose which one it wants.  In the current spec the
> server indicates which feature formats it supports for a particular
> versioned source as <FORMAT> subelements under a "Feature types"
> <NAMESPACE> element in the versioned source response.  I would like to
> change this so that the formats supported are specific to the type of
> feature.  This can be done by adding <FORMAT> subelements to the <TYPE>
> elements in the types response.  This would allow different alternative
> formats for different feature types, which I think is necessary -- a
> format optimized for SNPs is not going to be appropriate for serving up
> BLAT results, and vice versa.
> Now as far as the "compact" formats for other (non-feature) responses
> from the server, I don't think they're necessary.  As far as performance
> issues, the size of these responses are unlikely to be anywhere near as
> large as the potential responses from a features request.
> So to summarize, I think the spec definitely needs to support a
> mechanism for alternative feature formats, but that it should be
> agnostic as to what those formats are.  And I don't think we really need
> alternative formats for non-feature responses.
> 	gregg
> > -----Original Message-----
> > From: das2-bounces at portal.open-bio.org
> [mailto:das2-bounces at portal.open-
> > bio.org] On Behalf Of Andrew Dalke
> > Sent: Tuesday, May 17, 2005 11:14 AM
> > To: DAS/2
> > Subject: [DAS2] xml and compact formats
> >
> > Can someone remind me why we support both XML and "compact"
> > formats?  For what I'm doing it complicates things.  Was it
> > because of space/verbosity concerns?  If so, should we
> > encourage people to use compression on the connections?
> >
> > 					Andrew
> > 					dalke at dalkescientific.com
> >
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Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

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