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 _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
