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 :)
Cheers
Jonathan.
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" <[email protected]>
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
--
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Cancer Institute | 2000 Circle of Hope | SLC, UT 84112 | Rm: 3165
| Vc: 801.587.4611 | Fx: 801.585.6458 | [email protected] |
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" <[email protected]>
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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