[DAS] US DAS workshop

Tue Feb 22 18:10:11 UTC 2011

Just to add, the EBI will continue to support its SRA:
http://www.ebi.ac.uk/ena/SRA_announcement_Feb_2011.pdf

I have not heard of any DDBJ (also part of INSDC) plans to stop accepting submissions either. Is the availability of bandwidth workable for submissions at either of these? They should continue to sync as normal. I hear the east-west coast bandwidth isn't too great anyway, and the transatlantic link is OK.

On 22 Feb 2011, at 16:24, Ann Loraine wrote:

> The announcement says we can deposit RNA-Seq and epigenomic data to GEO and
> transcript assemblies to GenBank/TSA.
> 
> Will GEO capture and make available the FASTQ files? (Or some other format
> for reads?)
> 
> I like how easy GEO makes it to do a bulk download of CEL files.
> 
> Will it provide the same easy method for accessing FASTQ?
> 
> Tools in common use (e.g., bowtie, tophat) are changing at a lightning pace
> and it's important to have access to the "raw" sequence data well into the
> future. 
> 
> 
> On 2/22/11 11:05 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
> 
>> Sounds good Jonathan,
>> 
>> Thanks for pursuing this.  I would agree, there isn't a huge demand for a
>> general workshop (just yet) in the US.  Most bioinformatics folks I know just
>> haven't heard about DAS.  And even when I explain it to them the don't
>> understand it nor appreciate what a common language for data distribution can
>> do.  That will hopefully change....
>> 
>> Folks might not have heard but the SRA has been cut.
>> http://www.ncbi.nlm.nih.gov/sra for the official announcement and
>> http://seqanswers.com/forums/showthread.php?t=9431 for a thread on SeqAnswers.
>> This is the primary data repository for all things related to next generation
>> sequencing in the US. It's not clear where folks are going to put their fastq
>> and bam files.  It's kind of ridiculous how fragmented the data repository
>> problem has become. Here are the recommendations for where folks should bury,
>> I mean send their data in the US:
>> 
>> [cid:3381210354_50664721]
>> 
>> Ouch!  Each of these repositories has their own methods of encoding meta data
>> and distributing primary data and analysis. The data distribution problem is
>> becoming intractable.
>> 
>> I think we (DAS folks) should speak up loud and clear and make sure that DAS
>> is considered as a technology to link these disparate island of information.
>> 
>> -cheers, D
>> 
>> 
>> 
>> 
>> On 2/21/11 5:13 AM, "Jonathan Warren" <jw12 at sanger.ac.uk> wrote:
>> 
>> 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" <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
>>>>>>>> 
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> DAS mailing list
>>>>>>> DAS at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>>>> 
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> DAS mailing list
>>>>>>> DAS at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> --------------------------------------------------------------------------
>>>>>> ----
>>>>>> 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
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>> 
>>> 
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>> 
>> Jonathan Warren
>> Senior Developer and DAS coordinator
>> blog: http://biodasman.wordpress.com/
>> jw12 at sanger.ac.uk
>> Ext: 2314
>> Telephone: 01223 492314
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>> _______________________________________________
>> 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
> 