[DAS] using ProServer as a DAS source for IGB

[Gregg Helt]

You're not seeing DAS/2 in IGB because the use of DAS/2 has become an
integral part of IGB, to the point that it's no longer advertised as such.
This was partly motivated by feedback at Affymetrix (internally and from
customers) that DAS1, DAS/2, any mention of these things in IGB was just
confusing to users who didn't know what those were and didnt' really care
what protocol was being used, they just wanted to see the data.

So (unless you've tweaked some advanced prefs) when IGB first launches, goes
to a particular genome assembly, a particular chromosome, and pulls up the
chromosomal banding pattern and RefSeq annotations for that chromosome, all
that is happening via DAS/2.  The "Pick Genome" button that's used to switch
to a different genome assembly uses DAS/2.  The data access panel at the
bottom of IGB that allows you to select other annotation types to load is
using DAS/2.  The tricky bits of ID-to-genome-coordinate resolution that
happen behind the scenes if you load an Affymetrix gene or exon chp file
uses DAS/2.

Now there's a whole separate chunk of code in IGB that enables getting
annotations from DAS1 servers, which is accessed via the File-->"Access
DAS/1 Servers" menu item that you mention.  This is a much older code base,
and for some DAS1 servers it works, but for many others it doesn't.  For
your particular case I'm guessing that the IGB code is ignoring the
X-Das-Capabilities header and assuming that your server supports "types",
"features", and "entry_points" queries (or points to a MapMaster that
supports "entry_points" queries), and it's choking when it turns out the
server doesn't support either "types" or "entry_points".  This is definitely
a bug in IGB, and it didn't get fixed back when the IGB DAS1 client was
being developed because the DAS1 servers that most IGB users were accessing
at the time didn't trigger this bug.

Assuming the problem is with IGB's handling of DAS1 servers, there's several
possible solutions.

1) Configure your DAS server to support all three of the queries the IGB
DAS1 client needs: "types", "features", "entry_points".

2) Trellis/Ivy, the DAS1-->DAS2 proxy I've been developing, might work for
this situation.  Currently it probably won't, as the IGB DAS/2 client also
requires that the DAS/2 data sources support the DAS/2 "types" query.  But
this code base is evolving rapidly, and soon the proxy may be able to inject
type support for DAS1 servers that don't support "types" queries.  It
already does this kind of injection of the DAS/2 "segments" query for many
DAS1 sources in the Sanger DAS1 registry that don't list a
"das1:entry_points" capability.  One caveat to this approach is that
Trellis/Ivy supports the "sources" query but not the "dsn" query, and may
not ever since it looks like "dsn" may soon be deprecated.  Does ProServer
support the 1.53E "sources" query as an alternative to "dsn"?

3) Modify IGB so it can deal with DAS1 servers that don't support "types"
and "entry_points" queries.  But I'm reluctant to dive back into the old IGB
DAS1 code, and I doubt if anyone else wants to either.

4) Modify IGB so it can deal with DAS/2 servers that don't support "types"
and "segments" queries.  This is going to happen eventually, it's just a
question of timing.  Then Trellis/Ivy could be used as-is to proxy for the
DAS1 server and respons to IGB DAS/2 queries.

If it's straightforward to configure the DAS1 server to support "types" and
"entry_points" queries, then that's probably the quickest route.

One other caveat -- in order for IGB to overlay annotations from multiple
data sources, it needs to realize that they're using the same coordinate
system.  If coordinate system IDs don't match exactly, IGB uses a synonym
resolution strategy which usually relies on the synonyms doc at
http://netaffxdas.affymetrix.com/quickload_data/synonyms.txt .  If you can't
overlay annotations from multiple servers it's probably because their
coordinate IDs aren't listed as synonyms.  Let me and/or Steve Trutane know
(steve_chervitz at affymetrix.com) and he can add them in.  Hopefully increased
use of the DAS1 and DAS2 registries will lessen IGB's dependence on synonym
resolution.

      hope that helps,
      Gregg

On Mon, Oct 20, 2008 at 7:24 AM, Hotz, Hans-Rudolf
<hans-rudolf.hotz at fmi.ch>wrote:

> Hi
>
> Your e-mail was given to my by Andy Jenkinson one of the ProServer
> (http://www.sanger.ac.uk/Software/analysis/proserver/) developers at the
> EBI
> in Hinxton, UK).
>
> I am struggling to understand which DAS protocol is used in IGB. All the
> menu tabs are suggesting it is DAS/1 (eg File-> "Access DAS/1 Servers").
> But
> the release notes suggest is DAS/2. And if I try to load data from my
> ProServer I get:
>
>   Error parsing DAS Source
>   org.xml.sax.SAXParseException: Content is not allowed in prolog.
>
>
> Is there a way to use ProServer with IGB?
>
> Thank you very much for your help
>
> Hans
>
>
> Friedrich Miescher Institute
> for Biomedical Research
> Maulbeerstrasse 66
> 4058 Basel/Switzerland
>
>