So the current situation as far as I can see is that we have at least
two offers of venues to host a possible DAS workshop in the US. One
east coast and one west coast? Which is great.
However, at the moment we have no funding and we are not sure what
format the workshop should be.
I think Andy and myself are keen for this to happen in some way. Maybe
(after this workshop in the UK next week) we can come up with a short
5-10 question doodle poll that can be sent around to relevant email
lists in the US to get an idea of the likely attendance numbers, best
location, format and likely background of attendees etc.
This email discussion on the list hasn't convinced me that there is a
massive demand for a general workshop - however I would hope that at
the least Andy and myself would be able to come over and have a
developers meeting with the current active DAS developers..... So it
would be good to see what might come back from this doodle poll?
As a related topic: We are hoping to video many of the presentations
at the workshop next week to be made available shortly after over the
web. As always the tutorials and presentations will be available
online from the biodas wiki:
http://www.biodas.org/wiki/DASWorkshop2011
Hope to see some of you soon.
Thanks
Jonathan.
On 7 Feb 2011, at 18:00, Suzanna Lewis wrote:
On Feb 7, 2011, at 9:57 AM, Andy Jenkinson wrote:
Might we add on to the end/beginning of GI instead of running
concurrently (assuming CSHL can oblige)?
David Stewart is pretty open to this kind of thing given enough
forewarning.
Perhaps we can consider running a workshop at ISMB next year
(California?) should interest be sufficient for an event at GI or
the like this year?
ISMB is in California next year? Didn't know that. 2012 is far away
though.
I just noticed GI is actually in November though, by the way.
There is also biology of genomes in May.
On 7 Feb 2011, at 16:58, David Nix wrote:
Hmm...
There's the Genome Informatics meeting in August at CSHL ( http://meetings.cshl.edu/meetings/info11.shtml)
. It's not the bay area and the organizers might already have a
set program. There is a "Databases, Data Mining, Visualization
and Curation" session by Alex Bateman and Ting Wang though.
-cheers, D
On 2/7/11 9:25 AM, "Ann Loraine" <[email protected]> wrote:
Hi,
Same for us here at UNC Charlotte.
Meetings I'm attending next include two major plant science meetings
(Arabidopsis and ASPB) and possibly ISMB in Vienna.
David are there any other meetings you and your group are planning
to
attend?
The ideal setting would be a meeting where we can do outreach and
hold
workshop event(s) for users, but also have a developers meeting
where we
discuss future directions for the software, DAS spec, etc.
Are there other meetings that would be a good fit?
Best,
Ann
On 2/7/11 10:58 AM, "David Nix" <[email protected]> wrote:
Ah, that makes sense.
As for a US meeting, there are 3 or 4 folks here at the U of Utah
that would
attend an out of state meeting. The bay area would be ideal
(thanks Suzi!).
It might be best to make this part of a larger genomics/
proteomics meeting to
start. This would draw more folks who are interested in
distributing their
own data and working DAS access into their own applications. Are
their any
appropriate upcoming meetings?
-cheers, D
On 2/4/11 1:57 PM, "Andy Jenkinson" <[email protected]>
wrote:
Hi David,
I guess one of the big reasons to want a proxy is it allows you
to use DAS
sources you don't control, which is obviously potentially a
really big benefit
with so many DAS/1 sources around. I don't know if this is what
Jim is trying
to achieve though. In truth this has always been the difficulty
with the
das/das2 tech divide really, with such a huge existing
implementation base
there's a very high "activation energy" in switching!
What was the issue with the ensembl servers?
Jon and I have talked a few times about organising a DAS workshop
in North
America, we just need someone to host (and to an extent fund) it.
Do you have
any suggestions? Almost all of the attendees for our workshops
are from
Europe, in fact lots are from Hinxton. So what sort of demand do
you think
there would be stateside for such an event? Enough for a
standalone workshop,
or more conducive to an add-on to or collaboration with another
event?
Maybe we can look into webcasting the talks? No idea how to go
about this
though!
On 4 Feb 2011, at 19:13, David Nix wrote:
Hello Jim,
If I make a suggestion. If you're looking to visualize genomic
data in IGB,
it would be best to use a DAS/2 server such as the Classic
(command line) or
GenoPub (web app/ relational database) GenoViz DAS/2 server.
DAS/2 is well
suited to moving large amounts of sliced graph (gr, sgr,
bedgraph, wig, bar,
useq...) and alignment data (ie BAM) to client apps. We're
continuing to
develop the GenoPub DAS/2 server with 5 year grant support from
NHLBI so
expect continuing improvements (bulk uploading and file
conversion,
annotation via ontologies, super group visibility settings,
additional file
formats, etc.). See
http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2
and our paper
http://www.biomedcentral.com/1471-2105/11/455
GenoViz folks, correct me if I'm wrong here but I believe the
GenoViz DAS/2
server supports DAS xml datasets so moving data from a DAS/1
server to DAS/2
wouldn't require any data reformatting. Although for large
datasets, it's
best to use one of the compressed binary data formats such as
bar, bam, or
useq.
IGB comes pre configured with the UCSC and Ensembl DAS/1
servers. This works
well for accessing their small annotation datasets (gene models:
refseq,
knowngenes), but the graph distribution wasn't functional the
last I checked.
The problem appeared to be from the server side.
-cheers, David
P.S. I wish I could attend the DAS workshop this year and show
you what we've
been up to. Any chance of getting a Skype conference call with
posted
presentations? Would be great if someone hosted a DAS Workshop
in the US.
On 2/4/11 8:19 AM, "Gregg Helt" <[email protected]> wrote:
The core genomancer code is pretty stable, most of the recent
work is
in plugins (and some work in the core to allow more extensive
plugins).
You should be able to get a working DAS1-->DAS2 proxy running from
the current head of the Trellis SVN repository -- you would just
need
to add a web.xml config file with servlet parameters to get it
going in a
servlet container like Tomcat, or alternatively run the built-in
Jetty server
(ExampleJettyDas2Server) and edit servlet parameters directly in
code.
But if the intent is to load DAS 1.x data into IGB, I don't
think you
need to use Trellis. Th latest IGB (6.4.1 loaded via WebStart)
already supports DAS 1.5 access. In the "Data Access" tab, under
"Choose Data Sources and Data Sets" section click the "Configure"
button. This brings up a window with a "Data Sources" tab, and in
that tab you can click the "Add" button to bring up a dialog
that lets
you select "DAS" for the data source type, and enter the URL for
a DAS
server. This worked fine for loading data from the UCSC DAS 1.5
server -- I haven't tried accessing data from any other DAS
servers
recently.
I'm forwarding to the genoviz-devel list for IGB developments and
discussion, to see if anyone currently working on IGB can add
any more
info.
On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
<[email protected]> wrote:
Hi all (but Gregg in particular!)
I was wondering whether the DAS1 to DAS2 proxy component of
Trellis/Ivy
in the Genomancer project (http://code.google.com/p/
genomancer/) is
stable enough to use. We'd like to set up an in house DAS1->2
proxy and
it looks like there's a moderate amount of commit activity in the
project at the moment, making me a little nervous about
attempting to
use the code in a production(ish) setting.
many thanks in advance,
Jim.
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