[DAS] [Genoviz-devel] US DAS workshop

Andy Jenkinson andy.jenkinson at ebi.ac.uk
Wed Feb 9 17:19:12 UTC 2011 

Hi guys,

Just to mention, Mark Diekhans has kindly offered to help us arrange something at UCSC if we want, so we can consider that a solid offer. I shall defer to the Wisdom Of The List as to preference for location (no doubt Suzi would prefer Berkeley!). I'm not sure if the aim is to attract participation or just get together. Also, what sort of dates are people thinking of?

Cheers,
Andy

On 8 Feb 2011, at 21:49, Suzanna Lewis wrote:

> 
> 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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>>>> 
>>>> 
>>>> 
>>>> 
>> ----------------------------------------------------------------------------->>
>> -
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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
>> _______________________________________________
>> Genoviz-devel mailing list
>> Genoviz-devel at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>> 
>> 
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>

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