[DAS2] Minutes from 2 October 2008 DAS teleconference

[Gregg Helt]

Better-late-than-never minutes from 2 October 2008 DAS teleconference:

*Roll Call:*
Gregg Helt (unaffiliated: DAS/2, visualization, data modelling)
Suzi Lewis (LBNL: Apollo, etc.)
Ed Lee (LBNL: Apollo, annotation data models)
Ann Loraine (UNC: plant genomics, genomics vizualization)
Jon Nicols (UNC: genomics visualization )
Steven Blanchard (UNC: sys admin, security)
Andy Jenkinson (EBI: coordinator for DAS services at EBI)
Jonathon Warren (Sanger: coordinator for DAS services at Sanger)
Felix Kozinski (Sanger: DAS coordinator for Sanger ENCODE project)

*DAS/2 Status Summary:*
Gregg gave overview, refer to "DAS/2 Grant Final Progress Report" post
(October 2nd, 2008) on DAS/2 mailing list:
http://lists.open-bio.org/pipermail/das2/2008-October/000438.html
Stuff in summary not covered in progress report:
Alan Day is no longer at UCLA, and not working on the biopackages DAS/2
server (chado, BioPerl based DAS/2 server)
Possibility of deploying biopackages DAS/2 server on a MOD chado
installation (BOP? VectorBase?)
Several people at annotation workshop are using Apollo for curation
alongside IGB for viewing dense quantitative data.

*Hinxton DAS1 Summary*
Registry:
    now have DAS1 registry
    was one of the major things missing from DAS1 that motivated DAS2
    most clients use the registry
    about 400 sources in the registry
    implements validation
    uses same sources command as DAS/2
extensions
    alignments
    structures
    interactions
    in general evolving into a much wider system for biodata
core client/server implementations maintained at Sanger and EBI
lots of other implementations using DAS1, so heavy investment in DAS1
writeback
    one preliminary implementattion (partly based on DAS/2 writeback spec),
but nothing solid yet
    grant application being submitted December 8th
        collab between Sanger, EBI, and NBN (South Africa)
        includes writeback component (client and server implementations)
        client will be in DASTY
translation/bridge between protein and genomic space
        another goal of Sanger/EBI/NBN grant in preparation
Revising DAS1 spec (DAS 1.6)
    refer to biodas wiki pages:
        http://www.biodas.org/wiki/Spec_Review
        http://www.biodas.org/wiki/DAS_Plans
    no changes yet to sources, folded in as is from extensions, deprecate
dsn
"DAS is the general weapon of choice for integrating data throughout Sanger,
and largely at EBI as well"


*Other spec revision:*
DAS/2 spec frozen in November 2006, Gregg feels its time for revision
regardless of other integration, should make sure sources spec evolves in
sync between DAS1/2
Gregg's revisions: Two Plans
    #1.  DAS 2.1 --> relatively minor revisions to spec
    #2   no name yet --> much larger change
            possibly integrating DAS1 and DAS2
            move on top of Atom/AtomPub/GoogleData stack

*Andy -- DAS1 and DAS2*
    #2 above seems to be a good direction to go in from a technical
standpoint
    but, DAS/2 as it stands also seems to be good from a technical
standpoint
    major sticking point is backward compatibility with DAS1
    doesn't see how can convince powers that be to commit to DAS/2 without
backward compat
    other alternative is if there's a proxy that is very successful at DAS1
--> DAS/2 conversion
    Gregg -- still working on proxy, has expanded scope
            about a week away from usable
            proxy: DAS1.53 - dsn + sources
            source code going up on google code project hosting

*DAS2 Funding*
    Ann: recently awarded grant includes funding for DAS/2 arabidopsis
server
            wants to expand to cover many plants
            hopefully deployed at TAIR
            Suzi -- TAIR is using Apollo
            visualization
            UI improvements to IGB
            surveying different genomics visualization tools
            want to have easy way for small data providers to host data
            support/development of GenoViz toolkit
    Gregg:
           Lincoln committed to putting someone on DAS/2 client/server
support for GBrowse
           Gregg, Suzi, Ian Holmes discussing putting in distributed
annotation grant
                submit to NIH Feb 2009
                combine ideas and code from Apollo, JBrowse, IGB, DAS/2
                GMOD help desk now at UNC -- may be interested in joining in

    Andy -- prospects for grant focused on DAS itself as opposed to DAS
within other projects?
    Gregg -- problematic.  already had DAS/2 grant from NIH
    Suzi -- NIH now wants biology driving projects -- plain infrastructure
things don't tend to fly
    Gregg -- maybe could get funding again, but first need more results from
initial DAS/2 grant
                tried big reup three years ago, didn't fly
                need to get a paper out, more sites using
    Andy -- what would help is involvement of major institution
    Gregg -- but we tried with UCSC and PDB in reup, may have helped but
still didn't get funding
                involvement of major data repository necessary but not
sufficient for funding
    Andy -- in Europe industry partnership very important when asking for
funding now
            possibility of funding to build network of integrated EBI
resources based on DAS,
            that industry could use,
            possibility of money from UK/Europe, but probably need to use
what funding already have
    Ann -- what about developing a web services RCN (Research Coordination
Network) via NSF
            example: Microarray Coordination Network
            includes outreach
            in plant community people are using BioMoby a lot, but it's
complicated to use?
            Ann will look into NSF RCN funding possiblities
            iPlant (NSF)
    Sanger and EBI funding for DAS comes mostly from core informatics funds
    Andy -- discuss joining DAS1 and DAS2 in NSF proposal?
               would want institutes on both sides of the pond
    Suzi -- UCSC over here?
    Gregg -- I think they'd be amenable


*Action Items:
*schedule for DAS/2 teleconferences: every other Thursday @ 9AM PST
what are we talking about at the next one?
        get specific about specification changes
        start listing specific aims for grant proposals