[DAS] [Genoviz-devel] US DAS workshop

Tue Feb 8 19:44:03 UTC 2011

There are several of us here who are planning on attending with probably 2 talks and or posters (GenoPub, GNomEx and BST). Would be nice to have a talk on just DAS (history, apps, data sources, advantages/ disadvantages, DAS/1 vs DAS/2, future directions, etc.) even if the DAS workshop doesn't materialize.

Would someone who knows Tim or Alex be willing to approach them and inquire about the feasibility of a DAS workshop?

Suzi any more thoughts on a Bay Area session?

-cheers, D

On 2/7/11 11:02 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:

Hi,

Ting Wang is senior author on a Nature Methods review article (March 2010)
discussing visualization software for genomics.

The dates:

GENOME INFORMATICS
November 2 - 5, 2011
Abstract Deadline: August 12, 2011

I have a break from teaching in the fall so I will definitely try to attend.

The session on alternative splicing also looks very interesting.

Who in the developer's list is interested in attending, contributing to an
abstract, giving a talk?

Best wishes,

Ann

On 2/7/11 11:58 AM, "David Nix" <David.Nix at hci.utah.edu> 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" <aloraine at uncc.edu> 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" <David.Nix at hci.utah.edu> 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" <andy.jenkinson at ebi.ac.uk> 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" <gregghelt at gmail.com> 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
>>> <jprocter at compbio.dundee.ac.uk> 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.
>>>>
>>>> --
>>>> -------------------------------------------------------------------
>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>>
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>
>>>
>>> _______________________________________________
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>>>
>>>
>>> _______________________________________________
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>>
>>
>>
>>
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>
> --
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
>
>
>

--
Ann Loraine
Associate Professor
Dept. of Bioinformatics and Genomics, UNCC
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081
704-250-5750
www.transvar.org

------------------------------------------------------------------------------
The modern datacenter depends on network connectivity to access resources
and provide services. The best practices for maximizing a physical server's
connectivity to a physical network are well understood - see how these
rules translate into the virtual world?
http://p.sf.net/sfu/oracle-sfdevnlfb
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