[DAS] [Genoviz-devel] US DAS workshop

Suzanna Lewis suzi at berkeleybop.org
Sun Feb 13 10:42:33 UTC 2011 

UCSC is fine with me, and I don't even need to fly to get there. 

I'm also extremely happy if they and/or Mark Diekhans will take this on. Much easier for me to simply attend - I just wanted to be sure that the meeting happens.

In my head I was thinking of this largely as a developer's meeting/workshop for coordinating efforts.

-S


On Feb 11, 2011, at 3:13 PM, Ann Loraine wrote:

> I think it would be very helpful to have a meeting at UCSC.
> 
> UCSC is such an important data provider that it would be good for all of us
> to have more interactions with the team there.
> 
> Very best wishes,
> 
> Ann
> 
> 
> On 2/9/11 9:19 AM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
> 
>> 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
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>>>>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>>>>> 
>>>>>>> 
>>>>>>> _______________________________________________
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>>>>>>> 
>>>>>>> 
>>>>>>> _______________________________________________
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>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>> ----------------------------------------------------------------------------
>>>> ->>
>>>> -
>>>>>> 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
>>>>> 
>>>>> --
>>>>> 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
>>>> 
>>>> 
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>> 
>> 
> 
> -- 
> 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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