From ap3 at sanger.ac.uk Tue Apr 1 17:37:18 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Tue, 1 Apr 2008 22:37:18 +0100 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: References: Message-ID: <1F5A6606-0366-4697-815B-48EF79FC1824@sanger.ac.uk> Hi Steve, I don't really see the bifurcation between protein and genome DAS that you mention. We use DAS/1 nicely for both genome and protein clients. Also the DAS/1 extensions have been designed with being able to work with both worlds. The real bifurcation I see is the geographical split between the US and Europe as DAS is used in different ways here and there. Europe is very much organized around DAS/1. The ultimate goal of DAS is to separate data provision from visualization. As such a goal for us all should be that a DAS source can be shown in a similar fashion in all (genome) browsers. At the present this is not possible. In order to achieve such a standard it still will require a lot of collaboration, standardization and convincing between the different client and server-providers. Andreas > > There are perhaps are a handful of sites in the U.S. that have (or > are planning to) deploy DAS/2 servers in production environments, > though I don't have any official numbers. We've been tracking them > here: http://www.biodas.org/wiki/DAS/2#DAS.2F2_Servers > > Since the DAS/2 retrieval spec stabilized, there has been some work > on the writeback portion of the spec (for creating/editing > annotations), but that has not been finalized. As far as I know, it > hasn't progressed since the original grant for DAS/2 spec > development ended in Oct 2007. There was some good work done on the > writeback spec as well as some early implementations and it would > be good to see it congeal eventually. > > I know there's been continued development of the DAS/1 spec: http:// > www.dasregistry.org/spec_1.53E.jsp > > This has stirred up some thoughts I've been chewing on recently > regarding where DAS is headed. Comments welcome. Here goes: > > While it would be nice to see a single DAS spec to simplify the > lives of people writing clients and to unite development efforts, I > wonder if this is reasonable expect yet. The genome vs. protein > annotation bifurcation that we have now may reflect a natural > division that might be difficult to unite into a single spec. > However, I think the current state is more a matter of the large > amount of inertia behind DAS/1 -- the shear number of existing DAS/ > 1 servers and DAS/1 client code out there -- coupled with the fact > that DAS/2 is not backward compatible. Code doesn't rewrite itself. > > I know one of the early roadblocks for getting protein annotation > support into DAS/2 was that protein features were not described by > the Sequence Ontology (SO), but this has since been rectified. I've > learned that since August 2007, all of the protein features in the > bioSapiens project have been incorporated into SO ( http:// > www.dasregistry.org/extension_ontology.jsp ). > > The DAS/1 -> DAS/2 proxy adapter that Andrew Dalke worked on > ( http://lists.open-bio.org/pipermail/das2/2006-October/ > 000268.html ) could help with DAS/2 migration. But that project > never fully matured. Continued development of DAS/1 could > complicate the development of such an adapter. > > Regarding the genome-vs-protein DAS split, certainly there are many > commonalities at the level of annotations along a linear sequence > which apply equally well to nucleotide and protein sequences. Maybe > it would help to have a partitionable DAS spec to separate core > things from extensions that are nucleotide or protein-specific? > This could help isolate the more stable, low-level things from > higher-level functionality that is specific to nucleotide or > protein sequences, and could evolve without impacting the core > spec. A given DAS server would be compliant with the core and > either the genome or protein specific extensions of the spec. > > Cheers, > Steve > > > > From: Ann Loraine > > Date: Thu, 27 Mar 2008 10:04:21 -0400 > > To: Andreas Prlic > > Cc: Steve Chervitz , DAS/2 Discussion > > , > > Subject: Re: [DAS] DAS workshop presentations > > > > Regarding the funding issue: > > > > NSF is awarding me some funds that will support developing a > > Distributed Annotation Server to use for Arabidopsis data. (It is > > through the 2010 program.) > > > > DAS is not the main focus of the grant, but will play a big part > in what we > > do. > > > > I am also working on arranging a number we could use to carry on the > > DAS conference calls. > > > > Previously they were hosted by Affymetrix, but I think we can > probably > > do this for the group here at Charlotte. (I'm at University of North > > Carolina Charlotte.) > > > > All the best, > > > > Ann > > > > On Thu, Mar 27, 2008 at 9:35 AM, Andreas Prlic > wrote: > >> Hi Steve, > >> > >> We did not have an "official" slot for DAS/2, partially because we > >> did not have any DAS/2 related speakers. In the informal > discussions > >> some concern re DAS/2 was raised, > >> particularly about backwards compatibility issues and regarding > >> whether DAS/2 is still active and funded. > >> > >> Cheers, > >> Andreas > >> > >> > >> > >> > >> On 27 Mar 2008, at 01:24, Steve Chervitz wrote: > >> > >>> Thanks Andreas. Looks like you had a good workshop. > >>> Was there any discussion pertaining to DAS/2? > >>> > >>> Steve > >>> > >>>> From: Andreas Prlic > >>>> Date: Wed, 26 Mar 2008 16:01:26 +0000 > >>>> To: > >>>> Subject: [DAS] DAS workshop presentations > >>>> > >>>> Hi, > >>>> > >>>> We recently were hosting a DAS workshop at the Genome Campus in > >>>> Hinxton, U.K.. > >>>> > >>>> In case you are interested, the presentations of the first day > (DAS - > >>>> client developers day) are available from: > >>>> http://www..dasregistry.org/course.jsp > >>>> > >>>> The slides used for the second day (hands-on) are available from: > >>>> http://www.biodas.org/wiki/DASworkshop200802 > >>>> > >>>> Cheers, > >>>> Andreas > >>>> > >>>> > --------------------------------------------------------------------- > >>>> -- > >>>> > >>>> Andreas Prlic Wellcome Trust Sanger Institute > >>>> Hinxton, Cambridge CB10 1SA, UK > >>>> +44 (0) 1223 49 6891 > >>>> > >>>> > --------------------------------------------------------------------- > >>>> -- > >>>> > >>>> -- > >>>> 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 > >>> > >> > >> > ---------------------------------------------------------------------- > - > >> > >> Andreas Prlic Wellcome Trust Sanger Institute > >> Hinxton, Cambridge CB10 1SA, UK > >> +44 (0) 1223 49 6891 > >> > >> > ---------------------------------------------------------------------- > - > >> > >> > >> > >> > >> -- > >> 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 > >> > This transmission is intended for the sole use of the individual > and entity to whom it is addressed, and may contain information > that is privileged, confidential and exempt from disclosure under > applicable law. You are hereby notified that any use, > dissemination, distribution or duplication of this transmission by > someone other than the intended addressee or its designated agent > is strictly prohibited. If you have received this transmission in > error, please notify the sender immediately by reply to this > transmission and delete it from your computer. Thank You. > Affymetrix, Inc. ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- 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. From Steve_Chervitz at affymetrix.com Tue Apr 1 21:03:21 2008 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Tue, 01 Apr 2008 18:03:21 -0700 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: <1F5A6606-0366-4697-815B-48EF79FC1824@sanger.ac.uk> Message-ID: You're right. The bifurcation that has me concerned is really: DAS/1 --> genome & protein DAS/2 --> genome only Though DAS/2 can be used for protein sequence annotations, it has so far mainly (only?) been used for serving genome annotations. The retrieval DAS/2 spec itself is very genome-centric and could be updated/generalized to include protein examples. So I guess it's not so much a bifurcation but a disparity in level of support and usage patterns that distinguishes the 1 vs 2 versions of the spec, and this disparity seems destined to ensure the co-existence incompatible DAS 1 & 2 clients and servers. DAS/1 has a large installed base of servers and clients and the DAS/1 spec has more extensive support for protein sequence annotations. DAS/2 has some enhancements including support for alternative formats and an incipient writeback (annotation editing) facility. Usage as so far been confined to genome browsers. [ BTW: there isn't a good document describing these DAS/2 enhancements and how DAS/2 diverges from DAS/1. I'll try and put something up on the biodas.org wiki about this. In the meantime, there is a brief summary here: http://biodas.org/documents/das2/das2_protocol.html ] I agree with your ultimate goal for DAS. Getting there will take some effort, but promoting that vision is a important step. Resuming the conference calls as Ann mentioned will help. Cheers, Steve > From: Andreas Prlic > Date: Tue, 1 Apr 2008 22:37:18 +0100 > To: Steve Chervitz > Cc: DAS/2 Discussion , > Subject: Re: [DAS] DAS workshop presentations > > Hi Steve, > > I don't really see the bifurcation between protein and genome DAS > that you mention. We use DAS/1 nicely for both genome and protein > clients. > Also the DAS/1 extensions have been designed with being able to work > with both worlds. > > The real bifurcation I see is the geographical split between the US > and Europe as DAS is used in different ways here and there. Europe is > very much organized around DAS/1. > > The ultimate goal of DAS is to separate data provision from > visualization. As such a goal for us all should be that a DAS source > can be shown in a similar fashion in all (genome) browsers. At the > present this is not possible. In order to achieve such a standard it > still will require a lot of collaboration, standardization and > convincing between the different client and server-providers. > > Andreas > >> >> There are perhaps are a handful of sites in the U.S. that have (or >> are planning to) deploy DAS/2 servers in production environments, >> though I don't have any official numbers. We've been tracking them >> here: http://www.biodas.org/wiki/DAS/2#DAS.2F2_Servers >> >> Since the DAS/2 retrieval spec stabilized, there has been some work >> on the writeback portion of the spec (for creating/editing >> annotations), but that has not been finalized. As far as I know, it >> hasn't progressed since the original grant for DAS/2 spec >> development ended in Oct 2007. There was some good work done on the >> writeback spec as well as some early implementations and it would >> be good to see it congeal eventually. >> >> I know there's been continued development of the DAS/1 spec: http:// >> www.dasregistry.org/spec_1.53E.jsp >> >> This has stirred up some thoughts I've been chewing on recently >> regarding where DAS is headed. Comments welcome. Here goes: >> >> While it would be nice to see a single DAS spec to simplify the >> lives of people writing clients and to unite development efforts, I >> wonder if this is reasonable expect yet. The genome vs. protein >> annotation bifurcation that we have now may reflect a natural >> division that might be difficult to unite into a single spec. >> However, I think the current state is more a matter of the large >> amount of inertia behind DAS/1 -- the shear number of existing DAS/ >> 1 servers and DAS/1 client code out there -- coupled with the fact >> that DAS/2 is not backward compatible. Code doesn't rewrite itself. >> >> I know one of the early roadblocks for getting protein annotation >> support into DAS/2 was that protein features were not described by >> the Sequence Ontology (SO), but this has since been rectified. I've >> learned that since August 2007, all of the protein features in the >> bioSapiens project have been incorporated into SO ( http:// >> www.dasregistry.org/extension_ontology.jsp ). >> >> The DAS/1 -> DAS/2 proxy adapter that Andrew Dalke worked on >> ( http://lists.open-bio.org/pipermail/das2/2006-October/ >> 000268.html ) could help with DAS/2 migration. But that project >> never fully matured. Continued development of DAS/1 could >> complicate the development of such an adapter. >> >> Regarding the genome-vs-protein DAS split, certainly there are many >> commonalities at the level of annotations along a linear sequence >> which apply equally well to nucleotide and protein sequences. Maybe >> it would help to have a partitionable DAS spec to separate core >> things from extensions that are nucleotide or protein-specific? >> This could help isolate the more stable, low-level things from >> higher-level functionality that is specific to nucleotide or >> protein sequences, and could evolve without impacting the core >> spec. A given DAS server would be compliant with the core and >> either the genome or protein specific extensions of the spec. >> >> Cheers, >> Steve >> >> >>> From: Ann Loraine >>> Date: Thu, 27 Mar 2008 10:04:21 -0400 >>> To: Andreas Prlic >>> Cc: Steve Chervitz , DAS/2 Discussion >>> , >>> Subject: Re: [DAS] DAS workshop presentations >>> >>> Regarding the funding issue: >>> >>> NSF is awarding me some funds that will support developing a >>> Distributed Annotation Server to use for Arabidopsis data. (It is >>> through the 2010 program.) >>> >>> DAS is not the main focus of the grant, but will play a big part >> in what we >>> do. >>> >>> I am also working on arranging a number we could use to carry on the >>> DAS conference calls. >>> >>> Previously they were hosted by Affymetrix, but I think we can >> probably >>> do this for the group here at Charlotte. (I'm at University of North >>> Carolina Charlotte.) >>> >>> All the best, >>> >>> Ann >>> >>> On Thu, Mar 27, 2008 at 9:35 AM, Andreas Prlic >> wrote: >>>> Hi Steve, >>>> >>>> We did not have an "official" slot for DAS/2, partially because we >>>> did not have any DAS/2 related speakers. In the informal >> discussions >>>> some concern re DAS/2 was raised, >>>> particularly about backwards compatibility issues and regarding >>>> whether DAS/2 is still active and funded. >>>> >>>> Cheers, >>>> Andreas >>>> >>>> >>>> >>>> >>>> On 27 Mar 2008, at 01:24, Steve Chervitz wrote: >>>> >>>>> Thanks Andreas. Looks like you had a good workshop. >>>>> Was there any discussion pertaining to DAS/2? >>>>> >>>>> Steve >>>>> >>>>>> From: Andreas Prlic >>>>>> Date: Wed, 26 Mar 2008 16:01:26 +0000 >>>>>> To: >>>>>> Subject: [DAS] DAS workshop presentations >>>>>> >>>>>> Hi, >>>>>> >>>>>> We recently were hosting a DAS workshop at the Genome Campus in >>>>>> Hinxton, U.K.. >>>>>> >>>>>> In case you are interested, the presentations of the first day >> (DAS - >>>>>> client developers day) are available from: >>>>>> http://www..dasregistry.org/course.jsp >>>>>> >>>>>> The slides used for the second day (hands-on) are available from: >>>>>> http://www.biodas.org/wiki/DASworkshop200802 >>>>>> >>>>>> Cheers, >>>>>> Andreas >>>>>> >>>>>> >> --------------------------------------------------------------------- >>>>>> -- >>>>>> >>>>>> Andreas Prlic Wellcome Trust Sanger Institute >>>>>> Hinxton, Cambridge CB10 1SA, UK >>>>>> +44 (0) 1223 49 6891 >>>>>> >>>>>> >> --------------------------------------------------------------------- >>>>>> -- >>>>>> >>>>>> -- >>>>>> 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 >>>>> >>>> >>>> >> ---------------------------------------------------------------------- >> - >>>> >>>> Andreas Prlic Wellcome Trust Sanger Institute >>>> Hinxton, Cambridge CB10 1SA, UK >>>> +44 (0) 1223 49 6891 >>>> >>>> >> ---------------------------------------------------------------------- >> - >>>> >>>> >>>> >>>> >>>> -- >>>> 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 >>>> >> This transmission is intended for the sole use of the individual >> and entity to whom it is addressed, and may contain information >> that is privileged, confidential and exempt from disclosure under >> applicable law. You are hereby notified that any use, >> dissemination, distribution or duplication of this transmission by >> someone other than the intended addressee or its designated agent >> is strictly prohibited. If you have received this transmission in >> error, please notify the sender immediately by reply to this >> transmission and delete it from your computer. Thank You. >> Affymetrix, Inc. > > ----------------------------------------------------------------------- > > Andreas Prlic Wellcome Trust Sanger Institute > Hinxton, Cambridge CB10 1SA, UK > +44 (0) 1223 49 6891 > > ----------------------------------------------------------------------- > > > > > -- > 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. ------------------------------------------------------------ This transmission is intended for the sole use of the individual and entity to whom it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. You are hereby notified that any use, dissemination, distribution or duplication of this transmission by someone other than the intended addressee or its designated agent is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by reply to this transmission and delete it from your computer. Thank You. Affymetrix, Inc. From aloraine at gmail.com Tue Apr 1 23:16:29 2008 From: aloraine at gmail.com (Ann Loraine) Date: Tue, 1 Apr 2008 23:16:29 -0400 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: References: <1F5A6606-0366-4697-815B-48EF79FC1824@sanger.ac.uk> Message-ID: <83722dde0804012016o1c249176h754aeb04e8544a4e@mail.gmail.com> A compare/contrast document on DAS1/2 would be great. On a different note --- Does anyone know if the Gbrowse/GMOD system includes a DAS service? -Ann On Tue, Apr 1, 2008 at 9:03 PM, Steve Chervitz wrote: > You're right. The bifurcation that has me concerned is really: > > DAS/1 --> genome & protein > DAS/2 --> genome only > > Though DAS/2 can be used for protein sequence annotations, it has so far > mainly (only?) been used for serving genome annotations. The retrieval DAS/2 > spec itself is very genome-centric and could be updated/generalized to > include protein examples. > > So I guess it's not so much a bifurcation but a disparity in level of > support and usage patterns that distinguishes the 1 vs 2 versions of the > spec, and this disparity seems destined to ensure the co-existence > incompatible DAS 1 & 2 clients and servers. > > DAS/1 has a large installed base of servers and clients and the DAS/1 spec > has more extensive support for protein sequence annotations. > > DAS/2 has some enhancements including support for alternative formats and an > incipient writeback (annotation editing) facility. Usage as so far been > confined to genome browsers. > > [ BTW: there isn't a good document describing these DAS/2 enhancements and > how DAS/2 diverges from DAS/1. I'll try and put something up on the > biodas.org wiki about this. In the meantime, there is a brief summary here: > http://biodas.org/documents/das2/das2_protocol.html ] > > I agree with your ultimate goal for DAS. Getting there will take some > effort, but promoting that vision is a important step. Resuming the > conference calls as Ann mentioned will help. > > Cheers, > > Steve > > > > From: Andreas Prlic > > Date: Tue, 1 Apr 2008 22:37:18 +0100 > > To: Steve Chervitz > > Cc: DAS/2 Discussion , > > > > Subject: Re: [DAS] DAS workshop presentations > > > > Hi Steve, > > > > I don't really see the bifurcation between protein and genome DAS > > that you mention. We use DAS/1 nicely for both genome and protein > > clients. > > Also the DAS/1 extensions have been designed with being able to work > > with both worlds. > > > > The real bifurcation I see is the geographical split between the US > > and Europe as DAS is used in different ways here and there. Europe is > > very much organized around DAS/1. > > > > The ultimate goal of DAS is to separate data provision from > > visualization. As such a goal for us all should be that a DAS source > > can be shown in a similar fashion in all (genome) browsers. At the > > present this is not possible. In order to achieve such a standard it > > still will require a lot of collaboration, standardization and > > convincing between the different client and server-providers. > > > > Andreas > > > >> > >> There are perhaps are a handful of sites in the U.S. that have (or > >> are planning to) deploy DAS/2 servers in production environments, > >> though I don't have any official numbers. We've been tracking them > >> here: http://www.biodas.org/wiki/DAS/2#DAS.2F2_Servers > >> > >> Since the DAS/2 retrieval spec stabilized, there has been some work > >> on the writeback portion of the spec (for creating/editing > >> annotations), but that has not been finalized. As far as I know, it > >> hasn't progressed since the original grant for DAS/2 spec > >> development ended in Oct 2007. There was some good work done on the > >> writeback spec as well as some early implementations and it would > >> be good to see it congeal eventually. > >> > >> I know there's been continued development of the DAS/1 spec: http:// > >> www.dasregistry.org/spec_1.53E.jsp > >> > >> This has stirred up some thoughts I've been chewing on recently > >> regarding where DAS is headed. Comments welcome. Here goes: > >> > >> While it would be nice to see a single DAS spec to simplify the > >> lives of people writing clients and to unite development efforts, I > >> wonder if this is reasonable expect yet. The genome vs. protein > >> annotation bifurcation that we have now may reflect a natural > >> division that might be difficult to unite into a single spec. > >> However, I think the current state is more a matter of the large > >> amount of inertia behind DAS/1 -- the shear number of existing DAS/ > >> 1 servers and DAS/1 client code out there -- coupled with the fact > >> that DAS/2 is not backward compatible. Code doesn't rewrite itself. > >> > >> I know one of the early roadblocks for getting protein annotation > >> support into DAS/2 was that protein features were not described by > >> the Sequence Ontology (SO), but this has since been rectified. I've > >> learned that since August 2007, all of the protein features in the > >> bioSapiens project have been incorporated into SO ( http:// > >> www.dasregistry.org/extension_ontology.jsp ). > >> > >> The DAS/1 -> DAS/2 proxy adapter that Andrew Dalke worked on > >> ( http://lists.open-bio.org/pipermail/das2/2006-October/ > >> 000268.html ) could help with DAS/2 migration. But that project > >> never fully matured. Continued development of DAS/1 could > >> complicate the development of such an adapter. > >> > >> Regarding the genome-vs-protein DAS split, certainly there are many > >> commonalities at the level of annotations along a linear sequence > >> which apply equally well to nucleotide and protein sequences. Maybe > >> it would help to have a partitionable DAS spec to separate core > >> things from extensions that are nucleotide or protein-specific? > >> This could help isolate the more stable, low-level things from > >> higher-level functionality that is specific to nucleotide or > >> protein sequences, and could evolve without impacting the core > >> spec. A given DAS server would be compliant with the core and > >> either the genome or protein specific extensions of the spec. > >> > >> Cheers, > >> Steve > >> > >> > >>> From: Ann Loraine > >>> Date: Thu, 27 Mar 2008 10:04:21 -0400 > >>> To: Andreas Prlic > >>> Cc: Steve Chervitz , DAS/2 Discussion > >>> , > >>> Subject: Re: [DAS] DAS workshop presentations > >>> > >>> Regarding the funding issue: > >>> > >>> NSF is awarding me some funds that will support developing a > >>> Distributed Annotation Server to use for Arabidopsis data. (It is > >>> through the 2010 program.) > >>> > >>> DAS is not the main focus of the grant, but will play a big part > >> in what we > >>> do. > >>> > >>> I am also working on arranging a number we could use to carry on the > >>> DAS conference calls. > >>> > >>> Previously they were hosted by Affymetrix, but I think we can > >> probably > >>> do this for the group here at Charlotte. (I'm at University of North > >>> Carolina Charlotte.) > >>> > >>> All the best, > >>> > >>> Ann > >>> > >>> On Thu, Mar 27, 2008 at 9:35 AM, Andreas Prlic > >> wrote: > >>>> Hi Steve, > >>>> > >>>> We did not have an "official" slot for DAS/2, partially because we > >>>> did not have any DAS/2 related speakers. In the informal > >> discussions > >>>> some concern re DAS/2 was raised, > >>>> particularly about backwards compatibility issues and regarding > >>>> whether DAS/2 is still active and funded. > >>>> > >>>> Cheers, > >>>> Andreas > >>>> > >>>> > >>>> > >>>> > >>>> On 27 Mar 2008, at 01:24, Steve Chervitz wrote: > >>>> > >>>>> Thanks Andreas. Looks like you had a good workshop. > >>>>> Was there any discussion pertaining to DAS/2? > >>>>> > >>>>> Steve > >>>>> > >>>>>> From: Andreas Prlic > >>>>>> Date: Wed, 26 Mar 2008 16:01:26 +0000 > >>>>>> To: > >>>>>> Subject: [DAS] DAS workshop presentations > >>>>>> > >>>>>> Hi, > >>>>>> > >>>>>> We recently were hosting a DAS workshop at the Genome Campus in > >>>>>> Hinxton, U.K.. > >>>>>> > >>>>>> In case you are interested, the presentations of the first day > >> (DAS - > >>>>>> client developers day) are available from: > >>>>>> http://www..dasregistry.org/course.jsp > >>>>>> > >>>>>> The slides used for the second day (hands-on) are available from: > >>>>>> http://www.biodas.org/wiki/DASworkshop200802 > >>>>>> > >>>>>> Cheers, > >>>>>> Andreas > >>>>>> > >>>>>> > >> --------------------------------------------------------------------- > >>>>>> -- > >>>>>> > >>>>>> Andreas Prlic Wellcome Trust Sanger Institute > >>>>>> Hinxton, Cambridge CB10 1SA, UK > >>>>>> +44 (0) 1223 49 6891 > >>>>>> > >>>>>> > >> --------------------------------------------------------------------- > >>>>>> -- > >>>>>> > >>>>>> -- > >>>>>> 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 > >>>>> > >>>> > >>>> > >> ---------------------------------------------------------------------- > >> - > >>>> > >>>> Andreas Prlic Wellcome Trust Sanger Institute > >>>> Hinxton, Cambridge CB10 1SA, UK > >>>> +44 (0) 1223 49 6891 > >>>> > >>>> > >> ---------------------------------------------------------------------- > >> - > >>>> > >>>> > >>>> > >>>> > >>>> -- > >>>> 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 > >>>> > >> This transmission is intended for the sole use of the individual > >> and entity to whom it is addressed, and may contain information > >> that is privileged, confidential and exempt from disclosure under > >> applicable law. You are hereby notified that any use, > >> dissemination, distribution or duplication of this transmission by > >> someone other than the intended addressee or its designated agent > >> is strictly prohibited. If you have received this transmission in > >> error, please notify the sender immediately by reply to this > >> transmission and delete it from your computer. Thank You. > >> Affymetrix, Inc. > > > > ----------------------------------------------------------------------- > > > > Andreas Prlic Wellcome Trust Sanger Institute > > Hinxton, Cambridge CB10 1SA, UK > > +44 (0) 1223 49 6891 > > > > ----------------------------------------------------------------------- > > > > > > > > > > -- > > 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. > > > ------------------------------------------------------------ > > > This transmission is intended for the sole use of the individual > and entity to whom it is addressed, and may contain information > that is privileged, confidential and exempt from disclosure under > applicable law. You are hereby notified that any use, > dissemination, distribution or duplication of this transmission by > someone other than the intended addressee or its designated agent > is strictly prohibited. If you have received this transmission in > error, please notify the sender immediately by reply to this > transmission and delete it from your computer. Thank You. > Affymetrix, Inc. > > > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > From Steve_Chervitz at affymetrix.com Wed Apr 2 19:20:21 2008 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Wed, 02 Apr 2008 16:20:21 -0700 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: <3DFF95BA-9AA7-4FAA-B305-9825B9A8B6CD@ebi.ac.uk> Message-ID: Ewan Birney wrote on Wed, 2 Apr 2008 08:28:01 +0100: > On 2 Apr 2008, at 02:03, Steve Chervitz wrote: > >> You're right. The bifurcation that has me concerned is really: >> >> DAS/1 --> genome & protein >> DAS/2 --> genome only >> >> Though DAS/2 can be used for protein sequence annotations, it has >> so far >> mainly (only?) been used for serving genome annotations. The >> retrieval DAS/2 >> spec itself is very genome-centric and could be updated/generalized to >> include protein examples. >> >> So I guess it's not so much a bifurcation but a disparity in level of >> support and usage patterns that distinguishes the 1 vs 2 versions >> of the >> spec, and this disparity seems destined to ensure the co-existence >> incompatible DAS 1 & 2 clients and servers. >> >> DAS/1 has a large installed base of servers and clients and the DAS/ >> 1 spec >> has more extensive support for protein sequence annotations. >> >> DAS/2 has some enhancements including support for alternative >> formats and an >> incipient writeback (annotation editing) facility. Usage as so far >> been >> confined to genome browsers. >> > > One important thing in my mind is that "writeback" is a really huge > additional concept that carries so many semantic issues which many servers > just cannot implement (for sure, Ensembl is not going to be implementing > a writeback server in the near term). > > For me, DAS's sweet spot is a "dumb server, smart client" mode, where > there a few clients and many servers, and servers are easy to put up > etc. Write back requires smart(er) servers. > > So I would also advocate splitting the DAS/2 discussing into "read-only" > and "read-write" scenarios. I know this is implicitly there but I would > argue worth formalising at a higher level, and would stress the servers > can still be dumb. Agreed. Lots of issues involved with writeback. That portion of the DAS/2 spec is clearly segregated from the retrieval portion, and was still in the experimental stage when it was last worked on (~summer 2007). The future of this aspect of the spec isn't so clear to me. It would take a significant amount of developer time and community interest to make it fly. So I would de-emphasize the writeback stuff when discussing what DAS/2 brings to the table. Seems to me to be more important to first address how to best align the DAS/2 - DAS/1 work within the read-only world before getting into writeback, and only then if there's significant interest & funding. > It is also worth noting that DAS/1 has evolved as a "de facto", working > standard around the hinxton campus and we've really made good use and > built up momentum around it. It takes a long time bizarrely for people > to pick up technology and use it, and I want to make sure DAS/2 > discussion doesn't scare the growing set of people picking up and using > DAS/1 - which is very useful, pragmatic and critically has working > servers and clients now. The growth in DAS users is a good thing and should be encouraged since it helps realize the distributed annotation vision, and hooks up more people with more data. Whether DAS/1 or DAS/2 or DAS/n is used under the hood is a technical issue. One can always construct smarter clients that know how to speak whatever DAS flavor, though that's not necessarily a good long-term solution. It's clear that there is evolutionary pressure on the DAS spec, both in the existence of DAS/2 and in the modifications to DAS/1. What's less clear is how to channel these forces so that the innovative ideas on both sides of the pond can come together. Steve >> [ BTW: there isn't a good document describing these DAS/2 >> enhancements and >> how DAS/2 diverges from DAS/1. I'll try and put something up on the >> biodas.org wiki about this. In the meantime, there is a brief >> summary here: >> http://biodas.org/documents/das2/das2_protocol.html ] >> >> I agree with your ultimate goal for DAS. Getting there will take some >> effort, but promoting that vision is a important step. Resuming the >> conference calls as Ann mentioned will help. >> >> Cheers, >> Steve >> >> >>> From: Andreas Prlic >>> Date: Tue, 1 Apr 2008 22:37:18 +0100 >>> To: Steve Chervitz >>> Cc: DAS/2 Discussion , >>> Subject: Re: [DAS] DAS workshop presentations >>> >>> Hi Steve, >>> >>> I don't really see the bifurcation between protein and genome DAS >>> that you mention. We use DAS/1 nicely for both genome and protein >>> clients. >>> Also the DAS/1 extensions have been designed with being able to work >>> with both worlds. >>> >>> The real bifurcation I see is the geographical split between the US >>> and Europe as DAS is used in different ways here and there. Europe is >>> very much organized around DAS/1. >>> >>> The ultimate goal of DAS is to separate data provision from >>> visualization. As such a goal for us all should be that a DAS source >>> can be shown in a similar fashion in all (genome) browsers. At the >>> present this is not possible. In order to achieve such a standard it >>> still will require a lot of collaboration, standardization and >>> convincing between the different client and server-providers. >>> >>> Andreas >>> >>>> >>>> There are perhaps are a handful of sites in the U.S. that have (or >>>> are planning to) deploy DAS/2 servers in production environments, >>>> though I don't have any official numbers. We've been tracking them >>>> here: http://www.biodas.org/wiki/DAS/2#DAS.2F2_Servers >>>> >>>> Since the DAS/2 retrieval spec stabilized, there has been some work >>>> on the writeback portion of the spec (for creating/editing >>>> annotations), but that has not been finalized. As far as I know, it >>>> hasn't progressed since the original grant for DAS/2 spec >>>> development ended in Oct 2007. There was some good work done on the >>>> writeback spec as well as some early implementations and it would >>>> be good to see it congeal eventually. >>>> >>>> I know there's been continued development of the DAS/1 spec: http:// >>>> www.dasregistry.org/spec_1.53E.jsp >>>> >>>> This has stirred up some thoughts I've been chewing on recently >>>> regarding where DAS is headed. Comments welcome. Here goes: >>>> >>>> While it would be nice to see a single DAS spec to simplify the >>>> lives of people writing clients and to unite development efforts, I >>>> wonder if this is reasonable expect yet. The genome vs. protein >>>> annotation bifurcation that we have now may reflect a natural >>>> division that might be difficult to unite into a single spec. >>>> However, I think the current state is more a matter of the large >>>> amount of inertia behind DAS/1 -- the shear number of existing DAS/ >>>> 1 servers and DAS/1 client code out there -- coupled with the fact >>>> that DAS/2 is not backward compatible. Code doesn't rewrite itself. >>>> >>>> I know one of the early roadblocks for getting protein annotation >>>> support into DAS/2 was that protein features were not described by >>>> the Sequence Ontology (SO), but this has since been rectified. I've >>>> learned that since August 2007, all of the protein features in the >>>> bioSapiens project have been incorporated into SO ( http:// >>>> www.dasregistry.org/extension_ontology.jsp ). >>>> >>>> The DAS/1 -> DAS/2 proxy adapter that Andrew Dalke worked on >>>> ( http://lists.open-bio.org/pipermail/das2/2006-October/ >>>> 000268.html ) could help with DAS/2 migration. But that project >>>> never fully matured. Continued development of DAS/1 could >>>> complicate the development of such an adapter. >>>> >>>> Regarding the genome-vs-protein DAS split, certainly there are many >>>> commonalities at the level of annotations along a linear sequence >>>> which apply equally well to nucleotide and protein sequences. Maybe >>>> it would help to have a partitionable DAS spec to separate core >>>> things from extensions that are nucleotide or protein-specific? >>>> This could help isolate the more stable, low-level things from >>>> higher-level functionality that is specific to nucleotide or >>>> protein sequences, and could evolve without impacting the core >>>> spec. A given DAS server would be compliant with the core and >>>> either the genome or protein specific extensions of the spec. >>>> >>>> Cheers, >>>> Steve >>>> >>>> >>>>> From: Ann Loraine >>>>> Date: Thu, 27 Mar 2008 10:04:21 -0400 >>>>> To: Andreas Prlic >>>>> Cc: Steve Chervitz , DAS/2 >>>>> Discussion >>>>> , >>>>> Subject: Re: [DAS] DAS workshop presentations >>>>> >>>>> Regarding the funding issue: >>>>> >>>>> NSF is awarding me some funds that will support developing a >>>>> Distributed Annotation Server to use for Arabidopsis data. (It is >>>>> through the 2010 program.) >>>>> >>>>> DAS is not the main focus of the grant, but will play a big part >>>> in what we >>>>> do. >>>>> >>>>> I am also working on arranging a number we could use to carry on >>>>> the >>>>> DAS conference calls. >>>>> >>>>> Previously they were hosted by Affymetrix, but I think we can >>>> probably >>>>> do this for the group here at Charlotte. (I'm at University of >>>>> North >>>>> Carolina Charlotte.) >>>>> >>>>> All the best, >>>>> >>>>> Ann >>>>> >>>>> On Thu, Mar 27, 2008 at 9:35 AM, Andreas Prlic >>>> wrote: >>>>>> Hi Steve, >>>>>> >>>>>> We did not have an "official" slot for DAS/2, partially >>>>>> because we >>>>>> did not have any DAS/2 related speakers. In the informal >>>> discussions >>>>>> some concern re DAS/2 was raised, >>>>>> particularly about backwards compatibility issues and regarding >>>>>> whether DAS/2 is still active and funded. >>>>>> >>>>>> Cheers, >>>>>> Andreas >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 27 Mar 2008, at 01:24, Steve Chervitz wrote: >>>>>> >>>>>>> Thanks Andreas. Looks like you had a good workshop. >>>>>>> Was there any discussion pertaining to DAS/2? >>>>>>> >>>>>>> Steve >>>>>>> >>>>>>>> From: Andreas Prlic >>>>>>>> Date: Wed, 26 Mar 2008 16:01:26 +0000 >>>>>>>> To: >>>>>>>> Subject: [DAS] DAS workshop presentations >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> We recently were hosting a DAS workshop at the Genome Campus in >>>>>>>> Hinxton, U.K.. >>>>>>>> >>>>>>>> In case you are interested, the presentations of the first day >>>> (DAS - >>>>>>>> client developers day) are available from: >>>>>>>> http://www..dasregistry.org/course.jsp >>>>>>>> >>>>>>>> The slides used for the second day (hands-on) are available >>>>>>>> from: >>>>>>>> http://www.biodas.org/wiki/DASworkshop200802 >>>>>>>> >>>>>>>> Cheers, >>>>>>>> Andreas >>>>>>>> >>>>>>>> >>>> -------------------------------------------------------------------- >>>> - >>>>>>>> -- >>>>>>>> >>>>>>>> Andreas Prlic Wellcome Trust Sanger Institute >>>>>>>> Hinxton, Cambridge CB10 1SA, UK >>>>>>>> +44 (0) 1223 49 6891 >>>>>>>> >>>>>>>> >>>> -------------------------------------------------------------------- >>>> - >>>>>>>> -- >>>>>>>> >>>>>>>> -- >>>>>>>> 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 >>>>>>> >>>>>> >>>>>> >>>> -------------------------------------------------------------------- >>>> -- >>>> - >>>>>> >>>>>> Andreas Prlic Wellcome Trust Sanger Institute >>>>>> Hinxton, Cambridge CB10 1SA, UK >>>>>> +44 (0) 1223 49 6891 >>>>>> >>>>>> >>>> -------------------------------------------------------------------- >>>> -- >>>> - >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> 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 >>>>>> >>>> This transmission is intended for the sole use of the individual >>>> and entity to whom it is addressed, and may contain information >>>> that is privileged, confidential and exempt from disclosure under >>>> applicable law. You are hereby notified that any use, >>>> dissemination, distribution or duplication of this transmission by >>>> someone other than the intended addressee or its designated agent >>>> is strictly prohibited. If you have received this transmission in >>>> error, please notify the sender immediately by reply to this >>>> transmission and delete it from your computer. Thank You. >>>> Affymetrix, Inc. >>> >>> --------------------------------------------------------------------- >>> -- >>> >>> Andreas Prlic Wellcome Trust Sanger Institute >>> Hinxton, Cambridge CB10 1SA, UK >>> +44 (0) 1223 49 6891 >>> >>> --------------------------------------------------------------------- >>> -- >>> >>> >>> >>> >>> -- >>> 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. >> >> >> ------------------------------------------------------------ >> >> This transmission is intended for the sole use of the individual >> and entity to whom it is addressed, and may contain information >> that is privileged, confidential and exempt from disclosure under >> applicable law. You are hereby notified that any use, >> dissemination, distribution or duplication of this transmission by >> someone other than the intended addressee or its designated agent >> is strictly prohibited. If you have received this transmission in >> error, please notify the sender immediately by reply to this >> transmission and delete it from your computer. Thank You. >> Affymetrix, Inc. >> _______________________________________________ >> DAS mailing list >> DAS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das > From Steve_Chervitz at affymetrix.com Tue Apr 29 18:35:43 2008 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Tue, 29 Apr 2008 15:35:43 -0700 Subject: [DAS2] FW: BOSC 2008 Announcement and Call For Submissions In-Reply-To: <200804291659.m3TGxFZr020900@tenero.duhs.duke.edu> Message-ID: Sent on behalf of Darin London. ------ Forwarded Message > From: "darin.london at duke.edu" > Date: Tue, 29 Apr 2008 12:59:15 -0400 > To: > Subject: BOSC 2008 Announcement and Call For Submissions > > > BOSC 2008 Call for Abstracts Reminder > > The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take > place in Toronto, Ontario, Canada, as one of several Special Interest Group > (SIG) meetings occurring in conjunction with the 16th annual Intelligent > Systems for Molecular Biology Conference (ISMB 2008). > > This is a reminder to submit your proposals for talks to the BOSC submission > system before May 11. > > Submission Process: > All abstracts must be submitted through our Open Conference Systems site > (http://events.open-bio.org/BOSC2008/openconf.php). > The form will ask for a small Abstract Text to be pasted into it, and a full > paper. The small Abstract text should be a summary, while the longer abstract > (should provide more details, including the open-source license requirement > details) > Full-length abstracts are limited to one page with one inch (2.5 cm) margins > on the top, sides, and bottom. The full-length abstract should include the > title, authors, and affiliations. We prefer your abstract to be in PDF > format, although plain t > > Important Dates: > May 11: Abstract submission deadline. > June 2: Notification of accepted talks. > June 4: Early registration discount cut-off. > July 18-19: BOSC 2008! > > We hope to see you at BOSC 2008! > > Kam Dahlquist and Darin London > BOSC 2008 Co-organizers > > > ------ End of Forwarded Message ------------------------------------------------------------ This transmission is intended for the sole use of the individual and entity to whom it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. You are hereby notified that any use, dissemination, distribution or duplication of this transmission by someone other than the intended addressee or its designated agent is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by reply to this transmission and delete it from your computer. Thank You. Affymetrix, Inc. From Steve_Chervitz at affymetrix.com Tue Apr 1 01:51:46 2008 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Mon, 31 Mar 2008 18:51:46 -0700 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: <83722dde0803270704v338768e6p23aa4575738810d8@mail.gmail.com> Message-ID: Here are a few notes about DAS/2 activity: The DAS/2 retrieval spec for genome annotations has been stable and considered ready for production use since Nov 2006: http://biodas.org/documents/das2/das2_get.html There are perhaps are a handful of sites in the U.S. that have (or are planning to) deploy DAS/2 servers in production environments, though I don't have any official numbers. We've been tracking them here: http://www.biodas.org/wiki/DAS/2#DAS.2F2_Servers Since the DAS/2 retrieval spec stabilized, there has been some work on the writeback portion of the spec (for creating/editing annotations), but that has not been finalized. As far as I know, it hasn't progressed since the original grant for DAS/2 spec development ended in Oct 2007. There was some good work done on the writeback spec as well as some early implementations and it would be good to see it congeal eventually. I know there's been continued development of the DAS/1 spec: http://www.dasregistry.org/spec_1.53E.jsp This has stirred up some thoughts I've been chewing on recently regarding where DAS is headed. Comments welcome. Here goes: While it would be nice to see a single DAS spec to simplify the lives of people writing clients and to unite development efforts, I wonder if this is reasonable expect yet. The genome vs. protein annotation bifurcation that we have now may reflect a natural division that might be difficult to unite into a single spec. However, I think the current state is more a matter of the large amount of inertia behind DAS/1 -- the shear number of existing DAS/1 servers and DAS/1 client code out there -- coupled with the fact that DAS/2 is not backward compatible. Code doesn't rewrite itself. I know one of the early roadblocks for getting protein annotation support into DAS/2 was that protein features were not described by the Sequence Ontology (SO), but this has since been rectified. I've learned that since August 2007, all of the protein features in the bioSapiens project have been incorporated into SO ( http://www.dasregistry.org/extension_ontology.jsp ). The DAS/1 -> DAS/2 proxy adapter that Andrew Dalke worked on ( http://lists.open-bio.org/pipermail/das2/2006-October/000268.html ) could help with DAS/2 migration. But that project never fully matured. Continued development of DAS/1 could complicate the development of such an adapter. Regarding the genome-vs-protein DAS split, certainly there are many commonalities at the level of annotations along a linear sequence which apply equally well to nucleotide and protein sequences. Maybe it would help to have a partitionable DAS spec to separate core things from extensions that are nucleotide or protein-specific? This could help isolate the more stable, low-level things from higher-level functionality that is specific to nucleotide or protein sequences, and could evolve without impacting the core spec. A given DAS server would be compliant with the core and either the genome or protein specific extensions of the spec. Cheers, Steve > From: Ann Loraine > Date: Thu, 27 Mar 2008 10:04:21 -0400 > To: Andreas Prlic > Cc: Steve Chervitz , DAS/2 Discussion > , > Subject: Re: [DAS] DAS workshop presentations > > Regarding the funding issue: > > NSF is awarding me some funds that will support developing a > Distributed Annotation Server to use for Arabidopsis data. (It is > through the 2010 program.) > > DAS is not the main focus of the grant, but will play a big part in what we > do. > > I am also working on arranging a number we could use to carry on the > DAS conference calls. > > Previously they were hosted by Affymetrix, but I think we can probably > do this for the group here at Charlotte. (I'm at University of North > Carolina Charlotte.) > > All the best, > > Ann > > On Thu, Mar 27, 2008 at 9:35 AM, Andreas Prlic wrote: >> Hi Steve, >> >> We did not have an "official" slot for DAS/2, partially because we >> did not have any DAS/2 related speakers. In the informal discussions >> some concern re DAS/2 was raised, >> particularly about backwards compatibility issues and regarding >> whether DAS/2 is still active and funded. >> >> Cheers, >> Andreas >> >> >> >> >> On 27 Mar 2008, at 01:24, Steve Chervitz wrote: >> >>> Thanks Andreas. Looks like you had a good workshop. >>> Was there any discussion pertaining to DAS/2? >>> >>> Steve >>> >>>> From: Andreas Prlic >>>> Date: Wed, 26 Mar 2008 16:01:26 +0000 >>>> To: >>>> Subject: [DAS] DAS workshop presentations >>>> >>>> Hi, >>>> >>>> We recently were hosting a DAS workshop at the Genome Campus in >>>> Hinxton, U.K.. >>>> >>>> In case you are interested, the presentations of the first day (DAS - >>>> client developers day) are available from: >>>> http://www.dasregistry.org/course.jsp >>>> >>>> The slides used for the second day (hands-on) are available from: >>>> http://www.biodas.org/wiki/DASworkshop200802 >>>> >>>> Cheers, >>>> Andreas >>>> >>>> --------------------------------------------------------------------- >>>> -- >>>> >>>> Andreas Prlic Wellcome Trust Sanger Institute >>>> Hinxton, Cambridge CB10 1SA, UK >>>> +44 (0) 1223 49 6891 >>>> >>>> --------------------------------------------------------------------- >>>> -- >>>> >>>> -- >>>> 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 >>> >> >> ----------------------------------------------------------------------- >> >> Andreas Prlic Wellcome Trust Sanger Institute >> Hinxton, Cambridge CB10 1SA, UK >> +44 (0) 1223 49 6891 >> >> ----------------------------------------------------------------------- >> >> >> >> >> -- >> 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 >> ------------------------------------------------------------ This transmission is intended for the sole use of the individual and entity to whom it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. You are hereby notified that any use, dissemination, distribution or duplication of this transmission by someone other than the intended addressee or its designated agent is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by reply to this transmission and delete it from your computer. Thank You. Affymetrix, Inc. From ap3 at sanger.ac.uk Tue Apr 1 21:37:18 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Tue, 1 Apr 2008 22:37:18 +0100 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: References: Message-ID: <1F5A6606-0366-4697-815B-48EF79FC1824@sanger.ac.uk> Hi Steve, I don't really see the bifurcation between protein and genome DAS that you mention. We use DAS/1 nicely for both genome and protein clients. Also the DAS/1 extensions have been designed with being able to work with both worlds. The real bifurcation I see is the geographical split between the US and Europe as DAS is used in different ways here and there. Europe is very much organized around DAS/1. The ultimate goal of DAS is to separate data provision from visualization. As such a goal for us all should be that a DAS source can be shown in a similar fashion in all (genome) browsers. At the present this is not possible. In order to achieve such a standard it still will require a lot of collaboration, standardization and convincing between the different client and server-providers. Andreas > > There are perhaps are a handful of sites in the U.S. that have (or > are planning to) deploy DAS/2 servers in production environments, > though I don't have any official numbers. We've been tracking them > here: http://www.biodas.org/wiki/DAS/2#DAS.2F2_Servers > > Since the DAS/2 retrieval spec stabilized, there has been some work > on the writeback portion of the spec (for creating/editing > annotations), but that has not been finalized. As far as I know, it > hasn't progressed since the original grant for DAS/2 spec > development ended in Oct 2007. There was some good work done on the > writeback spec as well as some early implementations and it would > be good to see it congeal eventually. > > I know there's been continued development of the DAS/1 spec: http:// > www.dasregistry.org/spec_1.53E.jsp > > This has stirred up some thoughts I've been chewing on recently > regarding where DAS is headed. Comments welcome. Here goes: > > While it would be nice to see a single DAS spec to simplify the > lives of people writing clients and to unite development efforts, I > wonder if this is reasonable expect yet. The genome vs. protein > annotation bifurcation that we have now may reflect a natural > division that might be difficult to unite into a single spec. > However, I think the current state is more a matter of the large > amount of inertia behind DAS/1 -- the shear number of existing DAS/ > 1 servers and DAS/1 client code out there -- coupled with the fact > that DAS/2 is not backward compatible. Code doesn't rewrite itself. > > I know one of the early roadblocks for getting protein annotation > support into DAS/2 was that protein features were not described by > the Sequence Ontology (SO), but this has since been rectified. I've > learned that since August 2007, all of the protein features in the > bioSapiens project have been incorporated into SO ( http:// > www.dasregistry.org/extension_ontology.jsp ). > > The DAS/1 -> DAS/2 proxy adapter that Andrew Dalke worked on > ( http://lists.open-bio.org/pipermail/das2/2006-October/ > 000268.html ) could help with DAS/2 migration. But that project > never fully matured. Continued development of DAS/1 could > complicate the development of such an adapter. > > Regarding the genome-vs-protein DAS split, certainly there are many > commonalities at the level of annotations along a linear sequence > which apply equally well to nucleotide and protein sequences. Maybe > it would help to have a partitionable DAS spec to separate core > things from extensions that are nucleotide or protein-specific? > This could help isolate the more stable, low-level things from > higher-level functionality that is specific to nucleotide or > protein sequences, and could evolve without impacting the core > spec. A given DAS server would be compliant with the core and > either the genome or protein specific extensions of the spec. > > Cheers, > Steve > > > > From: Ann Loraine > > Date: Thu, 27 Mar 2008 10:04:21 -0400 > > To: Andreas Prlic > > Cc: Steve Chervitz , DAS/2 Discussion > > , > > Subject: Re: [DAS] DAS workshop presentations > > > > Regarding the funding issue: > > > > NSF is awarding me some funds that will support developing a > > Distributed Annotation Server to use for Arabidopsis data. (It is > > through the 2010 program.) > > > > DAS is not the main focus of the grant, but will play a big part > in what we > > do. > > > > I am also working on arranging a number we could use to carry on the > > DAS conference calls. > > > > Previously they were hosted by Affymetrix, but I think we can > probably > > do this for the group here at Charlotte. (I'm at University of North > > Carolina Charlotte.) > > > > All the best, > > > > Ann > > > > On Thu, Mar 27, 2008 at 9:35 AM, Andreas Prlic > wrote: > >> Hi Steve, > >> > >> We did not have an "official" slot for DAS/2, partially because we > >> did not have any DAS/2 related speakers. In the informal > discussions > >> some concern re DAS/2 was raised, > >> particularly about backwards compatibility issues and regarding > >> whether DAS/2 is still active and funded. > >> > >> Cheers, > >> Andreas > >> > >> > >> > >> > >> On 27 Mar 2008, at 01:24, Steve Chervitz wrote: > >> > >>> Thanks Andreas. Looks like you had a good workshop. > >>> Was there any discussion pertaining to DAS/2? > >>> > >>> Steve > >>> > >>>> From: Andreas Prlic > >>>> Date: Wed, 26 Mar 2008 16:01:26 +0000 > >>>> To: > >>>> Subject: [DAS] DAS workshop presentations > >>>> > >>>> Hi, > >>>> > >>>> We recently were hosting a DAS workshop at the Genome Campus in > >>>> Hinxton, U.K.. > >>>> > >>>> In case you are interested, the presentations of the first day > (DAS - > >>>> client developers day) are available from: > >>>> http://www..dasregistry.org/course.jsp > >>>> > >>>> The slides used for the second day (hands-on) are available from: > >>>> http://www.biodas.org/wiki/DASworkshop200802 > >>>> > >>>> Cheers, > >>>> Andreas > >>>> > >>>> > --------------------------------------------------------------------- > >>>> -- > >>>> > >>>> Andreas Prlic Wellcome Trust Sanger Institute > >>>> Hinxton, Cambridge CB10 1SA, UK > >>>> +44 (0) 1223 49 6891 > >>>> > >>>> > --------------------------------------------------------------------- > >>>> -- > >>>> > >>>> -- > >>>> 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 > >>> > >> > >> > ---------------------------------------------------------------------- > - > >> > >> Andreas Prlic Wellcome Trust Sanger Institute > >> Hinxton, Cambridge CB10 1SA, UK > >> +44 (0) 1223 49 6891 > >> > >> > ---------------------------------------------------------------------- > - > >> > >> > >> > >> > >> -- > >> 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 > >> > This transmission is intended for the sole use of the individual > and entity to whom it is addressed, and may contain information > that is privileged, confidential and exempt from disclosure under > applicable law. You are hereby notified that any use, > dissemination, distribution or duplication of this transmission by > someone other than the intended addressee or its designated agent > is strictly prohibited. If you have received this transmission in > error, please notify the sender immediately by reply to this > transmission and delete it from your computer. Thank You. > Affymetrix, Inc. ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- 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. From Steve_Chervitz at affymetrix.com Wed Apr 2 01:03:21 2008 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Tue, 01 Apr 2008 18:03:21 -0700 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: <1F5A6606-0366-4697-815B-48EF79FC1824@sanger.ac.uk> Message-ID: You're right. The bifurcation that has me concerned is really: DAS/1 --> genome & protein DAS/2 --> genome only Though DAS/2 can be used for protein sequence annotations, it has so far mainly (only?) been used for serving genome annotations. The retrieval DAS/2 spec itself is very genome-centric and could be updated/generalized to include protein examples. So I guess it's not so much a bifurcation but a disparity in level of support and usage patterns that distinguishes the 1 vs 2 versions of the spec, and this disparity seems destined to ensure the co-existence incompatible DAS 1 & 2 clients and servers. DAS/1 has a large installed base of servers and clients and the DAS/1 spec has more extensive support for protein sequence annotations. DAS/2 has some enhancements including support for alternative formats and an incipient writeback (annotation editing) facility. Usage as so far been confined to genome browsers. [ BTW: there isn't a good document describing these DAS/2 enhancements and how DAS/2 diverges from DAS/1. I'll try and put something up on the biodas.org wiki about this. In the meantime, there is a brief summary here: http://biodas.org/documents/das2/das2_protocol.html ] I agree with your ultimate goal for DAS. Getting there will take some effort, but promoting that vision is a important step. Resuming the conference calls as Ann mentioned will help. Cheers, Steve > From: Andreas Prlic > Date: Tue, 1 Apr 2008 22:37:18 +0100 > To: Steve Chervitz > Cc: DAS/2 Discussion , > Subject: Re: [DAS] DAS workshop presentations > > Hi Steve, > > I don't really see the bifurcation between protein and genome DAS > that you mention. We use DAS/1 nicely for both genome and protein > clients. > Also the DAS/1 extensions have been designed with being able to work > with both worlds. > > The real bifurcation I see is the geographical split between the US > and Europe as DAS is used in different ways here and there. Europe is > very much organized around DAS/1. > > The ultimate goal of DAS is to separate data provision from > visualization. As such a goal for us all should be that a DAS source > can be shown in a similar fashion in all (genome) browsers. At the > present this is not possible. In order to achieve such a standard it > still will require a lot of collaboration, standardization and > convincing between the different client and server-providers. > > Andreas > >> >> There are perhaps are a handful of sites in the U.S. that have (or >> are planning to) deploy DAS/2 servers in production environments, >> though I don't have any official numbers. We've been tracking them >> here: http://www.biodas.org/wiki/DAS/2#DAS.2F2_Servers >> >> Since the DAS/2 retrieval spec stabilized, there has been some work >> on the writeback portion of the spec (for creating/editing >> annotations), but that has not been finalized. As far as I know, it >> hasn't progressed since the original grant for DAS/2 spec >> development ended in Oct 2007. There was some good work done on the >> writeback spec as well as some early implementations and it would >> be good to see it congeal eventually. >> >> I know there's been continued development of the DAS/1 spec: http:// >> www.dasregistry.org/spec_1.53E.jsp >> >> This has stirred up some thoughts I've been chewing on recently >> regarding where DAS is headed. Comments welcome. Here goes: >> >> While it would be nice to see a single DAS spec to simplify the >> lives of people writing clients and to unite development efforts, I >> wonder if this is reasonable expect yet. The genome vs. protein >> annotation bifurcation that we have now may reflect a natural >> division that might be difficult to unite into a single spec. >> However, I think the current state is more a matter of the large >> amount of inertia behind DAS/1 -- the shear number of existing DAS/ >> 1 servers and DAS/1 client code out there -- coupled with the fact >> that DAS/2 is not backward compatible. Code doesn't rewrite itself. >> >> I know one of the early roadblocks for getting protein annotation >> support into DAS/2 was that protein features were not described by >> the Sequence Ontology (SO), but this has since been rectified. I've >> learned that since August 2007, all of the protein features in the >> bioSapiens project have been incorporated into SO ( http:// >> www.dasregistry.org/extension_ontology.jsp ). >> >> The DAS/1 -> DAS/2 proxy adapter that Andrew Dalke worked on >> ( http://lists.open-bio.org/pipermail/das2/2006-October/ >> 000268.html ) could help with DAS/2 migration. But that project >> never fully matured. Continued development of DAS/1 could >> complicate the development of such an adapter. >> >> Regarding the genome-vs-protein DAS split, certainly there are many >> commonalities at the level of annotations along a linear sequence >> which apply equally well to nucleotide and protein sequences. Maybe >> it would help to have a partitionable DAS spec to separate core >> things from extensions that are nucleotide or protein-specific? >> This could help isolate the more stable, low-level things from >> higher-level functionality that is specific to nucleotide or >> protein sequences, and could evolve without impacting the core >> spec. A given DAS server would be compliant with the core and >> either the genome or protein specific extensions of the spec. >> >> Cheers, >> Steve >> >> >>> From: Ann Loraine >>> Date: Thu, 27 Mar 2008 10:04:21 -0400 >>> To: Andreas Prlic >>> Cc: Steve Chervitz , DAS/2 Discussion >>> , >>> Subject: Re: [DAS] DAS workshop presentations >>> >>> Regarding the funding issue: >>> >>> NSF is awarding me some funds that will support developing a >>> Distributed Annotation Server to use for Arabidopsis data. (It is >>> through the 2010 program.) >>> >>> DAS is not the main focus of the grant, but will play a big part >> in what we >>> do. >>> >>> I am also working on arranging a number we could use to carry on the >>> DAS conference calls. >>> >>> Previously they were hosted by Affymetrix, but I think we can >> probably >>> do this for the group here at Charlotte. (I'm at University of North >>> Carolina Charlotte.) >>> >>> All the best, >>> >>> Ann >>> >>> On Thu, Mar 27, 2008 at 9:35 AM, Andreas Prlic >> wrote: >>>> Hi Steve, >>>> >>>> We did not have an "official" slot for DAS/2, partially because we >>>> did not have any DAS/2 related speakers. In the informal >> discussions >>>> some concern re DAS/2 was raised, >>>> particularly about backwards compatibility issues and regarding >>>> whether DAS/2 is still active and funded. >>>> >>>> Cheers, >>>> Andreas >>>> >>>> >>>> >>>> >>>> On 27 Mar 2008, at 01:24, Steve Chervitz wrote: >>>> >>>>> Thanks Andreas. Looks like you had a good workshop. >>>>> Was there any discussion pertaining to DAS/2? >>>>> >>>>> Steve >>>>> >>>>>> From: Andreas Prlic >>>>>> Date: Wed, 26 Mar 2008 16:01:26 +0000 >>>>>> To: >>>>>> Subject: [DAS] DAS workshop presentations >>>>>> >>>>>> Hi, >>>>>> >>>>>> We recently were hosting a DAS workshop at the Genome Campus in >>>>>> Hinxton, U.K.. >>>>>> >>>>>> In case you are interested, the presentations of the first day >> (DAS - >>>>>> client developers day) are available from: >>>>>> http://www..dasregistry.org/course.jsp >>>>>> >>>>>> The slides used for the second day (hands-on) are available from: >>>>>> http://www.biodas.org/wiki/DASworkshop200802 >>>>>> >>>>>> Cheers, >>>>>> Andreas >>>>>> >>>>>> >> --------------------------------------------------------------------- >>>>>> -- >>>>>> >>>>>> Andreas Prlic Wellcome Trust Sanger Institute >>>>>> Hinxton, Cambridge CB10 1SA, UK >>>>>> +44 (0) 1223 49 6891 >>>>>> >>>>>> >> --------------------------------------------------------------------- >>>>>> -- >>>>>> >>>>>> -- >>>>>> 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 >>>>> >>>> >>>> >> ---------------------------------------------------------------------- >> - >>>> >>>> Andreas Prlic Wellcome Trust Sanger Institute >>>> Hinxton, Cambridge CB10 1SA, UK >>>> +44 (0) 1223 49 6891 >>>> >>>> >> ---------------------------------------------------------------------- >> - >>>> >>>> >>>> >>>> >>>> -- >>>> 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 >>>> >> This transmission is intended for the sole use of the individual >> and entity to whom it is addressed, and may contain information >> that is privileged, confidential and exempt from disclosure under >> applicable law. You are hereby notified that any use, >> dissemination, distribution or duplication of this transmission by >> someone other than the intended addressee or its designated agent >> is strictly prohibited. If you have received this transmission in >> error, please notify the sender immediately by reply to this >> transmission and delete it from your computer. Thank You. >> Affymetrix, Inc. > > ----------------------------------------------------------------------- > > Andreas Prlic Wellcome Trust Sanger Institute > Hinxton, Cambridge CB10 1SA, UK > +44 (0) 1223 49 6891 > > ----------------------------------------------------------------------- > > > > > -- > 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. ------------------------------------------------------------ This transmission is intended for the sole use of the individual and entity to whom it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. You are hereby notified that any use, dissemination, distribution or duplication of this transmission by someone other than the intended addressee or its designated agent is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by reply to this transmission and delete it from your computer. Thank You. Affymetrix, Inc. From aloraine at gmail.com Wed Apr 2 03:16:29 2008 From: aloraine at gmail.com (Ann Loraine) Date: Tue, 1 Apr 2008 23:16:29 -0400 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: References: <1F5A6606-0366-4697-815B-48EF79FC1824@sanger.ac.uk> Message-ID: <83722dde0804012016o1c249176h754aeb04e8544a4e@mail.gmail.com> A compare/contrast document on DAS1/2 would be great. On a different note --- Does anyone know if the Gbrowse/GMOD system includes a DAS service? -Ann On Tue, Apr 1, 2008 at 9:03 PM, Steve Chervitz wrote: > You're right. The bifurcation that has me concerned is really: > > DAS/1 --> genome & protein > DAS/2 --> genome only > > Though DAS/2 can be used for protein sequence annotations, it has so far > mainly (only?) been used for serving genome annotations. The retrieval DAS/2 > spec itself is very genome-centric and could be updated/generalized to > include protein examples. > > So I guess it's not so much a bifurcation but a disparity in level of > support and usage patterns that distinguishes the 1 vs 2 versions of the > spec, and this disparity seems destined to ensure the co-existence > incompatible DAS 1 & 2 clients and servers. > > DAS/1 has a large installed base of servers and clients and the DAS/1 spec > has more extensive support for protein sequence annotations. > > DAS/2 has some enhancements including support for alternative formats and an > incipient writeback (annotation editing) facility. Usage as so far been > confined to genome browsers. > > [ BTW: there isn't a good document describing these DAS/2 enhancements and > how DAS/2 diverges from DAS/1. I'll try and put something up on the > biodas.org wiki about this. In the meantime, there is a brief summary here: > http://biodas.org/documents/das2/das2_protocol.html ] > > I agree with your ultimate goal for DAS. Getting there will take some > effort, but promoting that vision is a important step. Resuming the > conference calls as Ann mentioned will help. > > Cheers, > > Steve > > > > From: Andreas Prlic > > Date: Tue, 1 Apr 2008 22:37:18 +0100 > > To: Steve Chervitz > > Cc: DAS/2 Discussion , > > > > Subject: Re: [DAS] DAS workshop presentations > > > > Hi Steve, > > > > I don't really see the bifurcation between protein and genome DAS > > that you mention. We use DAS/1 nicely for both genome and protein > > clients. > > Also the DAS/1 extensions have been designed with being able to work > > with both worlds. > > > > The real bifurcation I see is the geographical split between the US > > and Europe as DAS is used in different ways here and there. Europe is > > very much organized around DAS/1. > > > > The ultimate goal of DAS is to separate data provision from > > visualization. As such a goal for us all should be that a DAS source > > can be shown in a similar fashion in all (genome) browsers. At the > > present this is not possible. In order to achieve such a standard it > > still will require a lot of collaboration, standardization and > > convincing between the different client and server-providers. > > > > Andreas > > > >> > >> There are perhaps are a handful of sites in the U.S. that have (or > >> are planning to) deploy DAS/2 servers in production environments, > >> though I don't have any official numbers. We've been tracking them > >> here: http://www.biodas.org/wiki/DAS/2#DAS.2F2_Servers > >> > >> Since the DAS/2 retrieval spec stabilized, there has been some work > >> on the writeback portion of the spec (for creating/editing > >> annotations), but that has not been finalized. As far as I know, it > >> hasn't progressed since the original grant for DAS/2 spec > >> development ended in Oct 2007. There was some good work done on the > >> writeback spec as well as some early implementations and it would > >> be good to see it congeal eventually. > >> > >> I know there's been continued development of the DAS/1 spec: http:// > >> www.dasregistry.org/spec_1.53E.jsp > >> > >> This has stirred up some thoughts I've been chewing on recently > >> regarding where DAS is headed. Comments welcome. Here goes: > >> > >> While it would be nice to see a single DAS spec to simplify the > >> lives of people writing clients and to unite development efforts, I > >> wonder if this is reasonable expect yet. The genome vs. protein > >> annotation bifurcation that we have now may reflect a natural > >> division that might be difficult to unite into a single spec. > >> However, I think the current state is more a matter of the large > >> amount of inertia behind DAS/1 -- the shear number of existing DAS/ > >> 1 servers and DAS/1 client code out there -- coupled with the fact > >> that DAS/2 is not backward compatible. Code doesn't rewrite itself. > >> > >> I know one of the early roadblocks for getting protein annotation > >> support into DAS/2 was that protein features were not described by > >> the Sequence Ontology (SO), but this has since been rectified. I've > >> learned that since August 2007, all of the protein features in the > >> bioSapiens project have been incorporated into SO ( http:// > >> www.dasregistry.org/extension_ontology.jsp ). > >> > >> The DAS/1 -> DAS/2 proxy adapter that Andrew Dalke worked on > >> ( http://lists.open-bio.org/pipermail/das2/2006-October/ > >> 000268.html ) could help with DAS/2 migration. But that project > >> never fully matured. Continued development of DAS/1 could > >> complicate the development of such an adapter. > >> > >> Regarding the genome-vs-protein DAS split, certainly there are many > >> commonalities at the level of annotations along a linear sequence > >> which apply equally well to nucleotide and protein sequences. Maybe > >> it would help to have a partitionable DAS spec to separate core > >> things from extensions that are nucleotide or protein-specific? > >> This could help isolate the more stable, low-level things from > >> higher-level functionality that is specific to nucleotide or > >> protein sequences, and could evolve without impacting the core > >> spec. A given DAS server would be compliant with the core and > >> either the genome or protein specific extensions of the spec. > >> > >> Cheers, > >> Steve > >> > >> > >>> From: Ann Loraine > >>> Date: Thu, 27 Mar 2008 10:04:21 -0400 > >>> To: Andreas Prlic > >>> Cc: Steve Chervitz , DAS/2 Discussion > >>> , > >>> Subject: Re: [DAS] DAS workshop presentations > >>> > >>> Regarding the funding issue: > >>> > >>> NSF is awarding me some funds that will support developing a > >>> Distributed Annotation Server to use for Arabidopsis data. (It is > >>> through the 2010 program.) > >>> > >>> DAS is not the main focus of the grant, but will play a big part > >> in what we > >>> do. > >>> > >>> I am also working on arranging a number we could use to carry on the > >>> DAS conference calls. > >>> > >>> Previously they were hosted by Affymetrix, but I think we can > >> probably > >>> do this for the group here at Charlotte. (I'm at University of North > >>> Carolina Charlotte.) > >>> > >>> All the best, > >>> > >>> Ann > >>> > >>> On Thu, Mar 27, 2008 at 9:35 AM, Andreas Prlic > >> wrote: > >>>> Hi Steve, > >>>> > >>>> We did not have an "official" slot for DAS/2, partially because we > >>>> did not have any DAS/2 related speakers. In the informal > >> discussions > >>>> some concern re DAS/2 was raised, > >>>> particularly about backwards compatibility issues and regarding > >>>> whether DAS/2 is still active and funded. > >>>> > >>>> Cheers, > >>>> Andreas > >>>> > >>>> > >>>> > >>>> > >>>> On 27 Mar 2008, at 01:24, Steve Chervitz wrote: > >>>> > >>>>> Thanks Andreas. Looks like you had a good workshop. > >>>>> Was there any discussion pertaining to DAS/2? > >>>>> > >>>>> Steve > >>>>> > >>>>>> From: Andreas Prlic > >>>>>> Date: Wed, 26 Mar 2008 16:01:26 +0000 > >>>>>> To: > >>>>>> Subject: [DAS] DAS workshop presentations > >>>>>> > >>>>>> Hi, > >>>>>> > >>>>>> We recently were hosting a DAS workshop at the Genome Campus in > >>>>>> Hinxton, U.K.. > >>>>>> > >>>>>> In case you are interested, the presentations of the first day > >> (DAS - > >>>>>> client developers day) are available from: > >>>>>> http://www..dasregistry.org/course.jsp > >>>>>> > >>>>>> The slides used for the second day (hands-on) are available from: > >>>>>> http://www.biodas.org/wiki/DASworkshop200802 > >>>>>> > >>>>>> Cheers, > >>>>>> Andreas > >>>>>> > >>>>>> > >> --------------------------------------------------------------------- > >>>>>> -- > >>>>>> > >>>>>> Andreas Prlic Wellcome Trust Sanger Institute > >>>>>> Hinxton, Cambridge CB10 1SA, UK > >>>>>> +44 (0) 1223 49 6891 > >>>>>> > >>>>>> > >> --------------------------------------------------------------------- > >>>>>> -- > >>>>>> > >>>>>> -- > >>>>>> 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 > >>>>> > >>>> > >>>> > >> ---------------------------------------------------------------------- > >> - > >>>> > >>>> Andreas Prlic Wellcome Trust Sanger Institute > >>>> Hinxton, Cambridge CB10 1SA, UK > >>>> +44 (0) 1223 49 6891 > >>>> > >>>> > >> ---------------------------------------------------------------------- > >> - > >>>> > >>>> > >>>> > >>>> > >>>> -- > >>>> 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 > >>>> > >> This transmission is intended for the sole use of the individual > >> and entity to whom it is addressed, and may contain information > >> that is privileged, confidential and exempt from disclosure under > >> applicable law. You are hereby notified that any use, > >> dissemination, distribution or duplication of this transmission by > >> someone other than the intended addressee or its designated agent > >> is strictly prohibited. If you have received this transmission in > >> error, please notify the sender immediately by reply to this > >> transmission and delete it from your computer. Thank You. > >> Affymetrix, Inc. > > > > ----------------------------------------------------------------------- > > > > Andreas Prlic Wellcome Trust Sanger Institute > > Hinxton, Cambridge CB10 1SA, UK > > +44 (0) 1223 49 6891 > > > > ----------------------------------------------------------------------- > > > > > > > > > > -- > > 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. > > > ------------------------------------------------------------ > > > This transmission is intended for the sole use of the individual > and entity to whom it is addressed, and may contain information > that is privileged, confidential and exempt from disclosure under > applicable law. You are hereby notified that any use, > dissemination, distribution or duplication of this transmission by > someone other than the intended addressee or its designated agent > is strictly prohibited. If you have received this transmission in > error, please notify the sender immediately by reply to this > transmission and delete it from your computer. Thank You. > Affymetrix, Inc. > > > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > From Steve_Chervitz at affymetrix.com Wed Apr 2 23:20:21 2008 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Wed, 02 Apr 2008 16:20:21 -0700 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: <3DFF95BA-9AA7-4FAA-B305-9825B9A8B6CD@ebi.ac.uk> Message-ID: Ewan Birney wrote on Wed, 2 Apr 2008 08:28:01 +0100: > On 2 Apr 2008, at 02:03, Steve Chervitz wrote: > >> You're right. The bifurcation that has me concerned is really: >> >> DAS/1 --> genome & protein >> DAS/2 --> genome only >> >> Though DAS/2 can be used for protein sequence annotations, it has >> so far >> mainly (only?) been used for serving genome annotations. The >> retrieval DAS/2 >> spec itself is very genome-centric and could be updated/generalized to >> include protein examples. >> >> So I guess it's not so much a bifurcation but a disparity in level of >> support and usage patterns that distinguishes the 1 vs 2 versions >> of the >> spec, and this disparity seems destined to ensure the co-existence >> incompatible DAS 1 & 2 clients and servers. >> >> DAS/1 has a large installed base of servers and clients and the DAS/ >> 1 spec >> has more extensive support for protein sequence annotations. >> >> DAS/2 has some enhancements including support for alternative >> formats and an >> incipient writeback (annotation editing) facility. Usage as so far >> been >> confined to genome browsers. >> > > One important thing in my mind is that "writeback" is a really huge > additional concept that carries so many semantic issues which many servers > just cannot implement (for sure, Ensembl is not going to be implementing > a writeback server in the near term). > > For me, DAS's sweet spot is a "dumb server, smart client" mode, where > there a few clients and many servers, and servers are easy to put up > etc. Write back requires smart(er) servers. > > So I would also advocate splitting the DAS/2 discussing into "read-only" > and "read-write" scenarios. I know this is implicitly there but I would > argue worth formalising at a higher level, and would stress the servers > can still be dumb. Agreed. Lots of issues involved with writeback. That portion of the DAS/2 spec is clearly segregated from the retrieval portion, and was still in the experimental stage when it was last worked on (~summer 2007). The future of this aspect of the spec isn't so clear to me. It would take a significant amount of developer time and community interest to make it fly. So I would de-emphasize the writeback stuff when discussing what DAS/2 brings to the table. Seems to me to be more important to first address how to best align the DAS/2 - DAS/1 work within the read-only world before getting into writeback, and only then if there's significant interest & funding. > It is also worth noting that DAS/1 has evolved as a "de facto", working > standard around the hinxton campus and we've really made good use and > built up momentum around it. It takes a long time bizarrely for people > to pick up technology and use it, and I want to make sure DAS/2 > discussion doesn't scare the growing set of people picking up and using > DAS/1 - which is very useful, pragmatic and critically has working > servers and clients now. The growth in DAS users is a good thing and should be encouraged since it helps realize the distributed annotation vision, and hooks up more people with more data. Whether DAS/1 or DAS/2 or DAS/n is used under the hood is a technical issue. One can always construct smarter clients that know how to speak whatever DAS flavor, though that's not necessarily a good long-term solution. It's clear that there is evolutionary pressure on the DAS spec, both in the existence of DAS/2 and in the modifications to DAS/1. What's less clear is how to channel these forces so that the innovative ideas on both sides of the pond can come together. Steve >> [ BTW: there isn't a good document describing these DAS/2 >> enhancements and >> how DAS/2 diverges from DAS/1. I'll try and put something up on the >> biodas.org wiki about this. In the meantime, there is a brief >> summary here: >> http://biodas.org/documents/das2/das2_protocol.html ] >> >> I agree with your ultimate goal for DAS. Getting there will take some >> effort, but promoting that vision is a important step. Resuming the >> conference calls as Ann mentioned will help. >> >> Cheers, >> Steve >> >> >>> From: Andreas Prlic >>> Date: Tue, 1 Apr 2008 22:37:18 +0100 >>> To: Steve Chervitz >>> Cc: DAS/2 Discussion , >>> Subject: Re: [DAS] DAS workshop presentations >>> >>> Hi Steve, >>> >>> I don't really see the bifurcation between protein and genome DAS >>> that you mention. We use DAS/1 nicely for both genome and protein >>> clients. >>> Also the DAS/1 extensions have been designed with being able to work >>> with both worlds. >>> >>> The real bifurcation I see is the geographical split between the US >>> and Europe as DAS is used in different ways here and there. Europe is >>> very much organized around DAS/1. >>> >>> The ultimate goal of DAS is to separate data provision from >>> visualization. As such a goal for us all should be that a DAS source >>> can be shown in a similar fashion in all (genome) browsers. At the >>> present this is not possible. In order to achieve such a standard it >>> still will require a lot of collaboration, standardization and >>> convincing between the different client and server-providers. >>> >>> Andreas >>> >>>> >>>> There are perhaps are a handful of sites in the U.S. that have (or >>>> are planning to) deploy DAS/2 servers in production environments, >>>> though I don't have any official numbers. We've been tracking them >>>> here: http://www.biodas.org/wiki/DAS/2#DAS.2F2_Servers >>>> >>>> Since the DAS/2 retrieval spec stabilized, there has been some work >>>> on the writeback portion of the spec (for creating/editing >>>> annotations), but that has not been finalized. As far as I know, it >>>> hasn't progressed since the original grant for DAS/2 spec >>>> development ended in Oct 2007. There was some good work done on the >>>> writeback spec as well as some early implementations and it would >>>> be good to see it congeal eventually. >>>> >>>> I know there's been continued development of the DAS/1 spec: http:// >>>> www.dasregistry.org/spec_1.53E.jsp >>>> >>>> This has stirred up some thoughts I've been chewing on recently >>>> regarding where DAS is headed. Comments welcome. Here goes: >>>> >>>> While it would be nice to see a single DAS spec to simplify the >>>> lives of people writing clients and to unite development efforts, I >>>> wonder if this is reasonable expect yet. The genome vs. protein >>>> annotation bifurcation that we have now may reflect a natural >>>> division that might be difficult to unite into a single spec. >>>> However, I think the current state is more a matter of the large >>>> amount of inertia behind DAS/1 -- the shear number of existing DAS/ >>>> 1 servers and DAS/1 client code out there -- coupled with the fact >>>> that DAS/2 is not backward compatible. Code doesn't rewrite itself. >>>> >>>> I know one of the early roadblocks for getting protein annotation >>>> support into DAS/2 was that protein features were not described by >>>> the Sequence Ontology (SO), but this has since been rectified. I've >>>> learned that since August 2007, all of the protein features in the >>>> bioSapiens project have been incorporated into SO ( http:// >>>> www.dasregistry.org/extension_ontology.jsp ). >>>> >>>> The DAS/1 -> DAS/2 proxy adapter that Andrew Dalke worked on >>>> ( http://lists.open-bio.org/pipermail/das2/2006-October/ >>>> 000268.html ) could help with DAS/2 migration. But that project >>>> never fully matured. Continued development of DAS/1 could >>>> complicate the development of such an adapter. >>>> >>>> Regarding the genome-vs-protein DAS split, certainly there are many >>>> commonalities at the level of annotations along a linear sequence >>>> which apply equally well to nucleotide and protein sequences. Maybe >>>> it would help to have a partitionable DAS spec to separate core >>>> things from extensions that are nucleotide or protein-specific? >>>> This could help isolate the more stable, low-level things from >>>> higher-level functionality that is specific to nucleotide or >>>> protein sequences, and could evolve without impacting the core >>>> spec. A given DAS server would be compliant with the core and >>>> either the genome or protein specific extensions of the spec. >>>> >>>> Cheers, >>>> Steve >>>> >>>> >>>>> From: Ann Loraine >>>>> Date: Thu, 27 Mar 2008 10:04:21 -0400 >>>>> To: Andreas Prlic >>>>> Cc: Steve Chervitz , DAS/2 >>>>> Discussion >>>>> , >>>>> Subject: Re: [DAS] DAS workshop presentations >>>>> >>>>> Regarding the funding issue: >>>>> >>>>> NSF is awarding me some funds that will support developing a >>>>> Distributed Annotation Server to use for Arabidopsis data. (It is >>>>> through the 2010 program.) >>>>> >>>>> DAS is not the main focus of the grant, but will play a big part >>>> in what we >>>>> do. >>>>> >>>>> I am also working on arranging a number we could use to carry on >>>>> the >>>>> DAS conference calls. >>>>> >>>>> Previously they were hosted by Affymetrix, but I think we can >>>> probably >>>>> do this for the group here at Charlotte. (I'm at University of >>>>> North >>>>> Carolina Charlotte.) >>>>> >>>>> All the best, >>>>> >>>>> Ann >>>>> >>>>> On Thu, Mar 27, 2008 at 9:35 AM, Andreas Prlic >>>> wrote: >>>>>> Hi Steve, >>>>>> >>>>>> We did not have an "official" slot for DAS/2, partially >>>>>> because we >>>>>> did not have any DAS/2 related speakers. In the informal >>>> discussions >>>>>> some concern re DAS/2 was raised, >>>>>> particularly about backwards compatibility issues and regarding >>>>>> whether DAS/2 is still active and funded. >>>>>> >>>>>> Cheers, >>>>>> Andreas >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 27 Mar 2008, at 01:24, Steve Chervitz wrote: >>>>>> >>>>>>> Thanks Andreas. Looks like you had a good workshop. >>>>>>> Was there any discussion pertaining to DAS/2? >>>>>>> >>>>>>> Steve >>>>>>> >>>>>>>> From: Andreas Prlic >>>>>>>> Date: Wed, 26 Mar 2008 16:01:26 +0000 >>>>>>>> To: >>>>>>>> Subject: [DAS] DAS workshop presentations >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> We recently were hosting a DAS workshop at the Genome Campus in >>>>>>>> Hinxton, U.K.. >>>>>>>> >>>>>>>> In case you are interested, the presentations of the first day >>>> (DAS - >>>>>>>> client developers day) are available from: >>>>>>>> http://www..dasregistry.org/course.jsp >>>>>>>> >>>>>>>> The slides used for the second day (hands-on) are available >>>>>>>> from: >>>>>>>> http://www.biodas.org/wiki/DASworkshop200802 >>>>>>>> >>>>>>>> Cheers, >>>>>>>> Andreas >>>>>>>> >>>>>>>> >>>> -------------------------------------------------------------------- >>>> - >>>>>>>> -- >>>>>>>> >>>>>>>> Andreas Prlic Wellcome Trust Sanger Institute >>>>>>>> Hinxton, Cambridge CB10 1SA, UK >>>>>>>> +44 (0) 1223 49 6891 >>>>>>>> >>>>>>>> >>>> -------------------------------------------------------------------- >>>> - >>>>>>>> -- >>>>>>>> >>>>>>>> -- >>>>>>>> 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 >>>>>>> >>>>>> >>>>>> >>>> -------------------------------------------------------------------- >>>> -- >>>> - >>>>>> >>>>>> Andreas Prlic Wellcome Trust Sanger Institute >>>>>> Hinxton, Cambridge CB10 1SA, UK >>>>>> +44 (0) 1223 49 6891 >>>>>> >>>>>> >>>> -------------------------------------------------------------------- >>>> -- >>>> - >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> 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 >>>>>> >>>> This transmission is intended for the sole use of the individual >>>> and entity to whom it is addressed, and may contain information >>>> that is privileged, confidential and exempt from disclosure under >>>> applicable law. You are hereby notified that any use, >>>> dissemination, distribution or duplication of this transmission by >>>> someone other than the intended addressee or its designated agent >>>> is strictly prohibited. If you have received this transmission in >>>> error, please notify the sender immediately by reply to this >>>> transmission and delete it from your computer. Thank You. >>>> Affymetrix, Inc. >>> >>> --------------------------------------------------------------------- >>> -- >>> >>> Andreas Prlic Wellcome Trust Sanger Institute >>> Hinxton, Cambridge CB10 1SA, UK >>> +44 (0) 1223 49 6891 >>> >>> --------------------------------------------------------------------- >>> -- >>> >>> >>> >>> >>> -- >>> 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. >> >> >> ------------------------------------------------------------ >> >> This transmission is intended for the sole use of the individual >> and entity to whom it is addressed, and may contain information >> that is privileged, confidential and exempt from disclosure under >> applicable law. You are hereby notified that any use, >> dissemination, distribution or duplication of this transmission by >> someone other than the intended addressee or its designated agent >> is strictly prohibited. If you have received this transmission in >> error, please notify the sender immediately by reply to this >> transmission and delete it from your computer. Thank You. >> Affymetrix, Inc. >> _______________________________________________ >> DAS mailing list >> DAS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das > From Steve_Chervitz at affymetrix.com Tue Apr 29 22:35:43 2008 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Tue, 29 Apr 2008 15:35:43 -0700 Subject: [DAS2] FW: BOSC 2008 Announcement and Call For Submissions In-Reply-To: <200804291659.m3TGxFZr020900@tenero.duhs.duke.edu> Message-ID: Sent on behalf of Darin London. ------ Forwarded Message > From: "darin.london at duke.edu" > Date: Tue, 29 Apr 2008 12:59:15 -0400 > To: > Subject: BOSC 2008 Announcement and Call For Submissions > > > BOSC 2008 Call for Abstracts Reminder > > The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take > place in Toronto, Ontario, Canada, as one of several Special Interest Group > (SIG) meetings occurring in conjunction with the 16th annual Intelligent > Systems for Molecular Biology Conference (ISMB 2008). > > This is a reminder to submit your proposals for talks to the BOSC submission > system before May 11. > > Submission Process: > All abstracts must be submitted through our Open Conference Systems site > (http://events.open-bio.org/BOSC2008/openconf.php). > The form will ask for a small Abstract Text to be pasted into it, and a full > paper. The small Abstract text should be a summary, while the longer abstract > (should provide more details, including the open-source license requirement > details) > Full-length abstracts are limited to one page with one inch (2.5 cm) margins > on the top, sides, and bottom. The full-length abstract should include the > title, authors, and affiliations. We prefer your abstract to be in PDF > format, although plain t > > Important Dates: > May 11: Abstract submission deadline. > June 2: Notification of accepted talks. > June 4: Early registration discount cut-off. > July 18-19: BOSC 2008! > > We hope to see you at BOSC 2008! > > Kam Dahlquist and Darin London > BOSC 2008 Co-organizers > > > ------ End of Forwarded Message ------------------------------------------------------------ This transmission is intended for the sole use of the individual and entity to whom it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. You are hereby notified that any use, dissemination, distribution or duplication of this transmission by someone other than the intended addressee or its designated agent is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by reply to this transmission and delete it from your computer. Thank You. Affymetrix, Inc.