[DAS2] using ProServer as a DAS source for IGB

[Ann Loraine]

I think Dr. Hotz is describing a difficulty many people have
experienced when working with IGB -- the various methods for loading
data into the browser are very confusing.

Here at Charlotte we're working on a new interface that aims to solve
this problem and make IGB much easier to operate.

One goal for the new data-loading interface is to let the user perform
essentially the same operations for loading data regardless of whether
the data are flowing from a DAS1 site, a DAS2 site, or from files on
the user's file system. (In the latter case, the user might need to
provide a simple file describing how the genome is put together, e.g.,
like the mod_chromInfo.txt from the old QuickLoad scheme.)

I'm working on a design document and will circulate it to anyone who
is interested in commenting or offering suggestions. Dr. Holtz please
let me know if this something you might like to do!

Sincerely,

Ann Loraine


On Wed, Oct 29, 2008 at 10:33 PM, Gregg Helt <gregghelt at gmail.com> wrote:
> 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
>>
>>
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