[DAS] alternative content

David Nix David.Nix at hci.utah.edu
Thu Sep 23 12:53:56 UTC 2010

Great!  Glad to hear it.  The faster alternative formats can be supported in DAS/1 the better.  DAS/1 can then be used for distributing dense genomic datasets. Bringing the two DAS protocols together would be a good thing.

I suppose then it just needs to be implemented using the 1.6E draft.

Any GenoViz developers want to volunteer to modify the DAS/1 servlet to support alternative formats?

-cheers, D

On 9/23/10 2:47 AM, "Jonathan Warren" <jw12 at sanger.ac.uk> wrote:

Hi David

Alternative content negotiation was discussed on day 3 of the DAS
workshop this year and proposed as a 1.6 Extension with a rough
outline of the specification here : http://www.biodas.org/wiki/DAS1.6E#Support_for_alternative_content_formats
. As far as I was aware it was pretty much agreed on subject to
testing in a real world example. This would allow you to use any
format you wish.... without affecting the workings of DAS servers and
clients already out in the wild.

If a group of developers want to develop it then we would wholly
support it as much as we are able here at Hinxton and I don't see any
barriers in any-ones way? Any necessary support would be put into the
dasregistry, in fact I was considering using JSON in the registry web
service and client javascript code just yesterday as well as xml. I
think this goes for any other useful extensions people wish to propose
and develop openly in the DAS community.

Just because something isn't in the 1.6 spec doesn't mean it can't be
developed and supported right now!

Hope to see you at the next DAS workshop :)



On 23 Sep 2010, at 00:29, Andy Jenkinson wrote:

> Hi David,
> For the avoidance of doubt, I am aware of no great reluctance to add
> alternative formats to DAS/1. In fact it is something I and others
> want to do and have wanted to do for a long time, we just haven't
> got around to it yet. So far, the maxbins extension has got us near
> enough and in truth just getting where we are with 1.6 (which is for
> the most part a consolidation of existing usage, with some
> exceptions) has been hard enough. That it is not in the 1.6
> specification should not be discouraging: for years major features
> of DAS as used by many, especially in Europe, were merely extensions
> to the core specification. Some of those are now becoming "core".
> The opportunity is there to implement it and the spec can be evolved
> accordingly so long as it is done "in the open". I would be happy to
> collaborate on it. One of the first things we wanted to do as a
> proof of principle and to establish a robust specification for
> negotiating content types was to have a JSON version of every
> command. IMO this would be a useful exercise in its own right which,
> as an addition to the binary formats, I daresay could drive quick
> adoption of alternative content types as a whole. Once the mechanism
> is decided, this example would also be quite easy to implement in
> servers and javascript-based clients such as those emerging recently.
> Our approach at Hinxton these days is somewhat pragmatic: if the
> spec needs to change to accomplish a real world goal, we will engage
> with the community to change it. But we do not tend to make
> speculative changes in the hope of them being used. In short, the
> possibility is there, it just needs someone to put their hand up and
> set about implementing it.
> By the way, what is the 2MB/s limitation you refer to?
> Cheers,
> Andy
> On 22 Sep 2010, at 21:33, David Nix wrote:
>> Bugger, that's unfortunate.  Without alternative formats, it is
>> impossible to distribute genomic data from next generation
>> sequencing and microarray experiments in a timely manner.  Even
>> then, the data transfer is very slow due to the <2MB/s bandwidth
>> limitation.
>> I wonder if folks should be encouraged to use DAS/2 for genomic
>> data distribution and DAS/1 for everything else?  There seems to be
>> a great reluctance to add alternative formats to DAS/1.  I can
>> understand the advantages of having a standardized data
>> distribution format.  Unfortunately this won't work for us, even
>> compressed, DAS GFF XML is about 100x larger than some of the other
>> binary genomic data formats such as bar and useq.
>> I'm afraid DAS is going to get left behind as other data
>> distribution models are adopted that can accommodate the ever
>> growing density of genomic data.
>> What do you think?
>> -cheers, D
>> On 9/22/10 10:51 AM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk>
>> wrote:
>> Hi David,
>> It is not part of DAS 1.6 but was discussed at the DAS workshop.
>> During the workshop we had some discussion on the topic and came up
>> with a couple of sensible proposals for an extension to 1.6 to
>> cover it. If my memory serves me we agreed on an outline proposal,
>> and there is a write up on http://www.biodas.org/wiki/DAS1.6E
>> (courtesy of Gregg? Is that correct?) but as far as I know there
>> are no implementations as yet.
>> Cheers,
>> Andy
>> On 22 Sep 2010, at 17:17, David Nix wrote:
>>> Hello Andy,
>>> I'm looking at the latest and trying to find out if alternative
>>> file formats were added to 1.6?  Can one respond to DAS/1 queries
>>> with binary data formats or is it still XML?  If the later, any
>>> time frame for when this will be added?
>>> -cheers, D
>>> --
>>> David Austin Nix, PhD | Bioinformatics Shared Resource | Huntsman
>>> Cancer Institute | 2000 Circle of Hope | SLC, UT 84112 | Rm: 3165
>>> | Vc: 801.587.4611 | Fx: 801.585.6458 | david.nix at hci.utah.edu |
>>> Skype/iChat: LiveNix | WebSite: http://bioserver.hci.utah.edu |
>>> DAS/2: http://bioserver.hci.utah.edu:8080/DAS2DB/genome
>>> On 9/22/10 9:44 AM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk>
>>> wrote:
>>> Hi all,
>>> I have updated the 1.6 specification to draft 7 in light of recent
>>> discussions on the list:
>>> 1. All features in a parent/part hierarchy must be returned if any
>>> overlap a query segment.
>>> 2. The alignment command is back to extension status, in
>>> anticipation of a revamp (see the 1.6E page on the wiki).
>>> Also in this draft is a previous change that was missed: the start
>>> and end attributes of a SEGMENT element in the features, types and
>>> entry_points commands are now optional. This makes it possible for
>>> servers without access to detailed information about the segments
>>> they are annotating to comply with the specification. Previously,
>>> it was impossible for such servers to respond in a compliant
>>> fashion to requests in which the client does not specify a start/
>>> end position.
>>> If my understanding is correct, no further changes to the
>>> specification are anticipated which means we can consider this the
>>> final draft...
>>> See here for details:
>>> http://www.biodas.org/wiki/DAS1.6
>>> Cheers,
>>> Andy
>>> _______________________________________________
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>>> DAS at lists.open-bio.org
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Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
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