[DAS] [Genoviz-devel] US DAS workshop

Tue Feb 8 21:49:20 UTC 2011

On Feb 8, 2011, at 2:44 PM, David Nix wrote:

> 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?
who? I probably should know who you're talking about, but they aren't part of the GI meeting or part of CSHL so ...

> 
> Suzi any more thoughts on a Bay Area session?

Given enough lead time there is a good room I can reserve for holding the meeting. So I suppose all that needs to be done at this point is for me to check availability of this room and given that, set up a doodle poll.

I'm assuming no more than 40 people. 

> 
> -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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>> 
>> --
>> 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
> 
> 
> 
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> 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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