From Steve_Chervitz at affymetrix.com Thu Mar 6 15:21:59 2008 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Thu, 06 Mar 2008 12:21:59 -0800 Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces In-Reply-To: <47C84F70.4000401@globalmentor.com> Message-ID: Hi Garret, As mentioned on the GlobalSeqIDs page: "The URLs do not need to be resolvable. At this point they are abstract identifiers." So they just happen to use ncbi, flybase, wormbase, etc. servers. In one sense, it doesn't matter what they are so long as all DAS servers that provide data for these assemblies consistently use them. To my knowledge, none of these organizations know that we are using their URI namespace in this way (except maybe for wormbase, which Lincoln -- who came up with these IDs -- works with). Is this a weakness? Perhaps. It's more a sign of the fact that most organizations are not yet clued into DAS. This issue harkens back to the URL-vs-URN-as-URI debate and whether URIs should be opaque, for example: http://rest.blueoxen.net/cgi-bin/wiki.pl?RestAndUriOpacity DAS has been designed with RESTful principles, so the abstractness requirement of the global seq IDs may seem unexpected. I can see some advantages of using the biodas.org namespace for these identifiers. The DAS maintainers would then be in control of managing any potential resolvability requirements. But given that we've already published these global seq IDs, I don't know the best route to change them should we decide to do so. If we published biodas.org-based URIs as synonyms to the current IDs, existing DAS/2 servers and clients (of which there aren't many yet) would need to be updated as well, to know that http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B33/ is equivalent to http://biodas.org/genome/H_sapiens/B33/, for example. Anyone else have thoughs/suggestions? Steve > From: Garret Wilson > Organization: GlobalMentor, Inc. > Date: Fri, 29 Feb 2008 10:31:12 -0800 > To: > Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces > > I read the "list of global identifiers based on community consensus" at: > > http://www.biodas.org/wiki/GlobalSeqIDs > > It's great the DAS/2 is using URIs for global identification. For > example, chromosome 1 for the B36.1 human genome assembly is identified > by the URI: > > http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B36.1/dna/chr1 > > I'm unclear, however, regarding NCBI knowledge, participation, and > maintenance of these URIs. The system of uniform resource identifiers > prevents name clashes by delegating to the IANA-governed domain-name > system, so that whoever owns a particular domain-based namespace can > manage the URIs within that namespace. > > If DAS/2 were to use, for example, the http://www.biodas.org/genome/ > namespace to manage all genome assembly URIs, I would have no cause for > concern. DAS/2 is instead using several namespaces managed by other > parties. I hope the response is that the NCBI is fully aware that its > URI namespace is being used as authoritative genome assembly URIs and > has either committed to maintaining that namespace or has delegated > maintenance of the http://www.ncbi.nlm.nih.gov/genome/ namespace to DAS. > (If the latter is true, it is unclear which organization would receive > such a delegation of maintenance responsibility---the Open > Bioinformatics Foundation? The BioTeam?) > > Thanks for any clarifications---this question is raised solely out of a > desire for long-term standards that can be use consistently by the > community. > > Garret > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 ------------------------------------------------------------ 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 garret at globalmentor.com Thu Mar 6 16:20:24 2008 From: garret at globalmentor.com (Garret Wilson) Date: Thu, 06 Mar 2008 13:20:24 -0800 Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces In-Reply-To: References: Message-ID: <47D06018.6010009@globalmentor.com> Hi, Steve! Thanks for the reply. The issue I raise is not resolvability---whether I can use an HTTP GET to retrieve some bytes at the location identified by the URI is a separate issue. Likewise the issue is not opacity---a genome assembly URI of would work just fine if we all agreed to use it. The issue I raise is solely that of URI namespace ownership and management. Let me give an example. Why don't we simply use the NCBI identifier "B36.1" to identify the latest Homo sapiens genome assembly, instead of inventing URIs to do the same thing? The answer is that "B36.1" has no managed namespace, so that anyone could use the identifier "B36.1" to identify anything---the flavor of a milkshake, for instance. Using URIs prevents clashes by dividing up the identifier space into namespaces, each managed by whoever is responsible for that namespace (based upon DNS managed by IANA). If someone who doesn't own a namespace (e.g. DAS2) starts reaching over into somebody else's namespace (e.g. NCBI) and starts using that namespace to create identifiers (e.g. ), then the namespace benefit of URIs has been negated. In fact, if the URIs are opaque and unresolvable, removing the benefit of namespace management means that URIs now have no benefit that I can think of over bare strings as IDs. That is my issue and concern. If the NCBI would come on board and start publishing URIs in its namespace to identify its genome assemblies (or even to officially ratify the URIs DAS2 has come up with), that would be ideal. If this doesn't happen, I'd recommend switching to URIs in a namespace DAS2 manages (producing e.g. or whatever.) Garret Steve Chervitz wrote: > Hi Garret, > > As mentioned on the GlobalSeqIDs page: > > "The URLs do not need to be resolvable. At this point they are abstract > identifiers." > > So they just happen to use ncbi, flybase, wormbase, etc. servers. In one > sense, it doesn't matter what they are so long as all DAS servers that > provide data for these assemblies consistently use them. > > To my knowledge, none of these organizations know that we are using their > URI namespace in this way (except maybe for wormbase, which Lincoln -- who > came up with these IDs -- works with). Is this a weakness? Perhaps. It's > more a sign of the fact that most organizations are not yet clued into DAS. > > This issue harkens back to the URL-vs-URN-as-URI debate and whether URIs > should be opaque, for example: > http://rest.blueoxen.net/cgi-bin/wiki.pl?RestAndUriOpacity > > DAS has been designed with RESTful principles, so the abstractness > requirement of the global seq IDs may seem unexpected. > > I can see some advantages of using the biodas.org namespace for these > identifiers. The DAS maintainers would then be in control of managing any > potential resolvability requirements. > > But given that we've already published these global seq IDs, I don't know > the best route to change them should we decide to do so. If we published > biodas.org-based URIs as synonyms to the current IDs, existing DAS/2 servers > and clients (of which there aren't many yet) would need to be updated as > well, to know that http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B33/ is > equivalent to http://biodas.org/genome/H_sapiens/B33/, for example. > > Anyone else have thoughs/suggestions? > > Steve > > >> From: Garret Wilson >> Organization: GlobalMentor, Inc. >> Date: Fri, 29 Feb 2008 10:31:12 -0800 >> To: >> Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces >> >> I read the "list of global identifiers based on community consensus" at: >> >> http://www.biodas.org/wiki/GlobalSeqIDs >> >> It's great the DAS/2 is using URIs for global identification. For >> example, chromosome 1 for the B36.1 human genome assembly is identified >> by the URI: >> >> http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B36.1/dna/chr1 >> >> I'm unclear, however, regarding NCBI knowledge, participation, and >> maintenance of these URIs. The system of uniform resource identifiers >> prevents name clashes by delegating to the IANA-governed domain-name >> system, so that whoever owns a particular domain-based namespace can >> manage the URIs within that namespace. >> >> If DAS/2 were to use, for example, the http://www.biodas.org/genome/ >> namespace to manage all genome assembly URIs, I would have no cause for >> concern. DAS/2 is instead using several namespaces managed by other >> parties. I hope the response is that the NCBI is fully aware that its >> URI namespace is being used as authoritative genome assembly URIs and >> has either committed to maintaining that namespace or has delegated >> maintenance of the http://www.ncbi.nlm.nih.gov/genome/ namespace to DAS. >> (If the latter is true, it is unclear which organization would receive >> such a delegation of maintenance responsibility---the Open >> Bioinformatics Foundation? The BioTeam?) >> >> Thanks for any clarifications---this question is raised solely out of a >> desire for long-term standards that can be use consistently by the >> community. >> >> Garret >> _______________________________________________ >> DAS2 mailing list >> DAS2 at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das2 >> > > > ------------------------------------------------------------ > > 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 garret at globalmentor.com Thu Mar 6 17:12:49 2008 From: garret at globalmentor.com (Garret Wilson) Date: Thu, 06 Mar 2008 14:12:49 -0800 Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces In-Reply-To: <95FDFF32-65BC-461E-A3D1-686992F865D1@fruitfly.org> References: <95FDFF32-65BC-461E-A3D1-686992F865D1@fruitfly.org> Message-ID: <47D06C61.7050805@globalmentor.com> Chris, Chris Mungall wrote: >> This issue harkens back to the URL-vs-URN-as-URI debate and whether URIs >> should be opaque, for example: >> http://rest.blueoxen.net/cgi-bin/wiki.pl?RestAndUriOpacity > > The debate has been raging on and off on various semantic web mail > lists over the years as well. Particularly the public-semweb-lifesci list Yes, I've watched those debates as well. But that's a debate that has nothing to do with the issue I raised here. > >> DAS has been designed with RESTful principles, so the abstractness >> requirement of the global seq IDs may seem unexpected. > > The consensus within the URL camp is that URLs should resolvable. I've even participated in this debate, arguing with a Nokia representative in the RDF community over whether HTTP URLs should be used for non-retrievable resources. But that's also completely ancillary to the point I raised. The point I raise here has to do with the legitimacy of using URIs in namespaces managed by third parties for a specification meant for global interoperability. It has nothing to do with opacity or resolvability of URIs. Garret From cjm at fruitfly.org Thu Mar 6 17:02:18 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 6 Mar 2008 14:02:18 -0800 Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces In-Reply-To: References: Message-ID: <95FDFF32-65BC-461E-A3D1-686992F865D1@fruitfly.org> On Mar 6, 2008, at 12:21 PM, Steve Chervitz wrote: > Hi Garret, > > As mentioned on the GlobalSeqIDs page: > > "The URLs do not need to be resolvable. At this point they are > abstract > identifiers." > > So they just happen to use ncbi, flybase, wormbase, etc. servers. > In one > sense, it doesn't matter what they are so long as all DAS servers that > provide data for these assemblies consistently use them. > > To my knowledge, none of these organizations know that we are using > their > URI namespace in this way (except maybe for wormbase, which Lincoln > -- who > came up with these IDs -- works with). Is this a weakness? Perhaps. > It's > more a sign of the fact that most organizations are not yet clued > into DAS. > > This issue harkens back to the URL-vs-URN-as-URI debate and whether > URIs > should be opaque, for example: > http://rest.blueoxen.net/cgi-bin/wiki.pl?RestAndUriOpacity The debate has been raging on and off on various semantic web mail lists over the years as well. Particularly the public-semweb-lifesci list The consensus appears to be URLs over non-URL URIs (though consensus is not necessarily right), though Mark W (guessing you're on this list Mark?) and others favour LSIDs. > DAS has been designed with RESTful principles, so the abstractness > requirement of the global seq IDs may seem unexpected. The consensus within the URL camp is that URLs should resolvable. So the DAS/2 approach of using URLs for which it would be difficult to guarantee resolvability would appear to be out of step with both camps. > I can see some advantages of using the biodas.org namespace for these > identifiers. The DAS maintainers would then be in control of > managing any > potential resolvability requirements. > But given that we've already published these global seq IDs, I > don't know > the best route to change them should we decide to do so. If we > published > biodas.org-based URIs as synonyms to the current IDs, existing DAS/ > 2 servers > and clients (of which there aren't many yet) would need to be > updated as > well, to know that http://www.ncbi.nlm.nih.gov/genome/H_sapiens/ > B33/ is > equivalent to http://biodas.org/genome/H_sapiens/B33/, for example. My feeling is that officially granted identifiers such as NC_000001.9 (current build of H_sapiens chr1) should be used where possible, with URIs constructed using some external registry of databases; eg http://www.geneontology.org/cgi-bin/xrefs.cgi However, there is clearly a need for a RESTful way of referring to sequence assemblies keyed by organism, build and chromosome, along the lines mentioned above. This could be a useful service of biodas.org I'm not sure if some notion of URI synonyms is built into DAS/2. This could perhaps be done externally via URL redirects and/or RDF metadata > Anyone else have thoughs/suggestions? > > Steve > >> From: Garret Wilson >> Organization: GlobalMentor, Inc. >> Date: Fri, 29 Feb 2008 10:31:12 -0800 >> To: >> Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces >> >> I read the "list of global identifiers based on community >> consensus" at: >> >> http://www.biodas.org/wiki/GlobalSeqIDs >> >> It's great the DAS/2 is using URIs for global identification. For >> example, chromosome 1 for the B36.1 human genome assembly is >> identified >> by the URI: >> >> http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B36.1/dna/chr1 >> >> I'm unclear, however, regarding NCBI knowledge, participation, and >> maintenance of these URIs. The system of uniform resource identifiers >> prevents name clashes by delegating to the IANA-governed domain-name >> system, so that whoever owns a particular domain-based namespace can >> manage the URIs within that namespace. >> >> If DAS/2 were to use, for example, the http://www.biodas.org/genome/ >> namespace to manage all genome assembly URIs, I would have no >> cause for >> concern. DAS/2 is instead using several namespaces managed by other >> parties. I hope the response is that the NCBI is fully aware that its >> URI namespace is being used as authoritative genome assembly URIs and >> has either committed to maintaining that namespace or has delegated >> maintenance of the http://www.ncbi.nlm.nih.gov/genome/ namespace >> to DAS. >> (If the latter is true, it is unclear which organization would >> receive >> such a delegation of maintenance responsibility---the Open >> Bioinformatics Foundation? The BioTeam?) >> >> Thanks for any clarifications---this question is raised solely out >> of a >> desire for long-term standards that can be use consistently by the >> community. >> >> Garret >> _______________________________________________ >> DAS2 mailing list >> DAS2 at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das2 > > > ------------------------------------------------------------ > > 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 Fri Mar 21 15:48:56 2008 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Fri, 21 Mar 2008 12:48:56 -0700 Subject: [DAS2] BOSC 2008 Announcement and Call For Submissions Message-ID: [Sent on behalf of Darin London ] BOSC 2008 Call for Abstracts 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). The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. Many Open Source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation and dissemination of new computational methods as well as informatics infrastructure. Since the work of the Open Source Bioinformatics Community represents some of the most cutting edge of Bioinformatics in general, the overall theme for the conference this year is "Tackling Hard Problems with Emerging Technologies". Topics under this umbrella include cyberinfrastructure, grid computing and workflow management and discovery, and visualization. We will also have a s! eries of update talks about the main Open Source Bioinformatics Software suites. One of the hallmarks of BOSC is the coming together of the open source developer community in one location. A face-to-face meeting of this community creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done. This year, BOSC is accepting abstract submissions on the conference theme "Tackling Hard Problems with Emerging Technologies". The conference theme reflects that there are new technologies emerging on both the scientific front (new sequencing technologies, etc.) and the IT front (workflows, mashup/web 2.0, improvements in all of the major programming languages, etc.), which may allow the open source community to solve problems that were previously intractable. Abstracts may be submitted for the following topics. 1. Cyberinfrastructure - We are interested in presentations on topics dealing with the development of infrastructure on the web to facilitate software and data re-use (mashups, or traditional), interoperability and inter-process communication, system/service discovery, and data movement and modeling in distributed systems. This may include peer-to-peer systems of data transfer, Web Services, various flavors of data representation (SOAP, JSON, XML, others), and technologies commonly referred to under the Web 2.0 paradigm (e.g. folksonomies/tagging, user-based content generation, content feeds, and Social Networking). 2. Grid Computing and Workflow Management and Discovery - We particularly invite talks that report progress in making workflow systems easier to use and on how to do distributed-collaborative research , e.g. workflows that encompass the coordination of systems running in different parts of the world. 3. Visualization - Visualization is a maturing area of open source software development. We particularly invite talks that demonstrate innovative visualization systems in the context of workflows. 4. Open Source Software - Speakers will present talks on the use, development, or philosophy of open source software in bioinformatics. 5. Bio* Open Source Project Updates - We invite abstracts from the representatives of the open source projects sponsored by or affiliated to the O|B|F (see Projects). Please consult the official BOSC 2008 website at http://www.open-bio.org/wiki/Upcoming_BOSC_conference for all updates and extra information. 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 ------------------------------------------------------------ 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 Wed Mar 26 21:24:18 2008 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Wed, 26 Mar 2008 18:24:18 -0700 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: <51CB8D74-3F41-4AD1-B4DC-F99A459C4E19@sanger.ac.uk> Message-ID: 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 From ap3 at sanger.ac.uk Thu Mar 27 09:35:26 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Thu, 27 Mar 2008 13:35:26 +0000 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: References: Message-ID: 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. From aloraine at gmail.com Thu Mar 27 10:04:21 2008 From: aloraine at gmail.com (Ann Loraine) Date: Thu, 27 Mar 2008 10:04:21 -0400 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: References:

Message-ID: <83722dde0803270704v338768e6p23aa4575738810d8@mail.gmail.com> 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 > From Steve_Chervitz at affymetrix.com Mon Mar 31 21:51:46 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 Steve_Chervitz at affymetrix.com Thu Mar 6 20:21:59 2008 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Thu, 06 Mar 2008 12:21:59 -0800 Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces In-Reply-To: <47C84F70.4000401@globalmentor.com> Message-ID: Hi Garret, As mentioned on the GlobalSeqIDs page: "The URLs do not need to be resolvable. At this point they are abstract identifiers." So they just happen to use ncbi, flybase, wormbase, etc. servers. In one sense, it doesn't matter what they are so long as all DAS servers that provide data for these assemblies consistently use them. To my knowledge, none of these organizations know that we are using their URI namespace in this way (except maybe for wormbase, which Lincoln -- who came up with these IDs -- works with). Is this a weakness? Perhaps. It's more a sign of the fact that most organizations are not yet clued into DAS. This issue harkens back to the URL-vs-URN-as-URI debate and whether URIs should be opaque, for example: http://rest.blueoxen.net/cgi-bin/wiki.pl?RestAndUriOpacity DAS has been designed with RESTful principles, so the abstractness requirement of the global seq IDs may seem unexpected. I can see some advantages of using the biodas.org namespace for these identifiers. The DAS maintainers would then be in control of managing any potential resolvability requirements. But given that we've already published these global seq IDs, I don't know the best route to change them should we decide to do so. If we published biodas.org-based URIs as synonyms to the current IDs, existing DAS/2 servers and clients (of which there aren't many yet) would need to be updated as well, to know that http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B33/ is equivalent to http://biodas.org/genome/H_sapiens/B33/, for example. Anyone else have thoughs/suggestions? Steve > From: Garret Wilson > Organization: GlobalMentor, Inc. > Date: Fri, 29 Feb 2008 10:31:12 -0800 > To: > Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces > > I read the "list of global identifiers based on community consensus" at: > > http://www.biodas.org/wiki/GlobalSeqIDs > > It's great the DAS/2 is using URIs for global identification. For > example, chromosome 1 for the B36.1 human genome assembly is identified > by the URI: > > http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B36.1/dna/chr1 > > I'm unclear, however, regarding NCBI knowledge, participation, and > maintenance of these URIs. The system of uniform resource identifiers > prevents name clashes by delegating to the IANA-governed domain-name > system, so that whoever owns a particular domain-based namespace can > manage the URIs within that namespace. > > If DAS/2 were to use, for example, the http://www.biodas.org/genome/ > namespace to manage all genome assembly URIs, I would have no cause for > concern. DAS/2 is instead using several namespaces managed by other > parties. I hope the response is that the NCBI is fully aware that its > URI namespace is being used as authoritative genome assembly URIs and > has either committed to maintaining that namespace or has delegated > maintenance of the http://www.ncbi.nlm.nih.gov/genome/ namespace to DAS. > (If the latter is true, it is unclear which organization would receive > such a delegation of maintenance responsibility---the Open > Bioinformatics Foundation? The BioTeam?) > > Thanks for any clarifications---this question is raised solely out of a > desire for long-term standards that can be use consistently by the > community. > > Garret > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 ------------------------------------------------------------ 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 garret at globalmentor.com Thu Mar 6 21:20:24 2008 From: garret at globalmentor.com (Garret Wilson) Date: Thu, 06 Mar 2008 13:20:24 -0800 Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces In-Reply-To: References: Message-ID: <47D06018.6010009@globalmentor.com> Hi, Steve! Thanks for the reply. The issue I raise is not resolvability---whether I can use an HTTP GET to retrieve some bytes at the location identified by the URI is a separate issue. Likewise the issue is not opacity---a genome assembly URI of would work just fine if we all agreed to use it. The issue I raise is solely that of URI namespace ownership and management. Let me give an example. Why don't we simply use the NCBI identifier "B36.1" to identify the latest Homo sapiens genome assembly, instead of inventing URIs to do the same thing? The answer is that "B36.1" has no managed namespace, so that anyone could use the identifier "B36.1" to identify anything---the flavor of a milkshake, for instance. Using URIs prevents clashes by dividing up the identifier space into namespaces, each managed by whoever is responsible for that namespace (based upon DNS managed by IANA). If someone who doesn't own a namespace (e.g. DAS2) starts reaching over into somebody else's namespace (e.g. NCBI) and starts using that namespace to create identifiers (e.g. ), then the namespace benefit of URIs has been negated. In fact, if the URIs are opaque and unresolvable, removing the benefit of namespace management means that URIs now have no benefit that I can think of over bare strings as IDs. That is my issue and concern. If the NCBI would come on board and start publishing URIs in its namespace to identify its genome assemblies (or even to officially ratify the URIs DAS2 has come up with), that would be ideal. If this doesn't happen, I'd recommend switching to URIs in a namespace DAS2 manages (producing e.g. or whatever.) Garret Steve Chervitz wrote: > Hi Garret, > > As mentioned on the GlobalSeqIDs page: > > "The URLs do not need to be resolvable. At this point they are abstract > identifiers." > > So they just happen to use ncbi, flybase, wormbase, etc. servers. In one > sense, it doesn't matter what they are so long as all DAS servers that > provide data for these assemblies consistently use them. > > To my knowledge, none of these organizations know that we are using their > URI namespace in this way (except maybe for wormbase, which Lincoln -- who > came up with these IDs -- works with). Is this a weakness? Perhaps. It's > more a sign of the fact that most organizations are not yet clued into DAS. > > This issue harkens back to the URL-vs-URN-as-URI debate and whether URIs > should be opaque, for example: > http://rest.blueoxen.net/cgi-bin/wiki.pl?RestAndUriOpacity > > DAS has been designed with RESTful principles, so the abstractness > requirement of the global seq IDs may seem unexpected. > > I can see some advantages of using the biodas.org namespace for these > identifiers. The DAS maintainers would then be in control of managing any > potential resolvability requirements. > > But given that we've already published these global seq IDs, I don't know > the best route to change them should we decide to do so. If we published > biodas.org-based URIs as synonyms to the current IDs, existing DAS/2 servers > and clients (of which there aren't many yet) would need to be updated as > well, to know that http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B33/ is > equivalent to http://biodas.org/genome/H_sapiens/B33/, for example. > > Anyone else have thoughs/suggestions? > > Steve > > >> From: Garret Wilson >> Organization: GlobalMentor, Inc. >> Date: Fri, 29 Feb 2008 10:31:12 -0800 >> To: >> Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces >> >> I read the "list of global identifiers based on community consensus" at: >> >> http://www.biodas.org/wiki/GlobalSeqIDs >> >> It's great the DAS/2 is using URIs for global identification. For >> example, chromosome 1 for the B36.1 human genome assembly is identified >> by the URI: >> >> http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B36.1/dna/chr1 >> >> I'm unclear, however, regarding NCBI knowledge, participation, and >> maintenance of these URIs. The system of uniform resource identifiers >> prevents name clashes by delegating to the IANA-governed domain-name >> system, so that whoever owns a particular domain-based namespace can >> manage the URIs within that namespace. >> >> If DAS/2 were to use, for example, the http://www.biodas.org/genome/ >> namespace to manage all genome assembly URIs, I would have no cause for >> concern. DAS/2 is instead using several namespaces managed by other >> parties. I hope the response is that the NCBI is fully aware that its >> URI namespace is being used as authoritative genome assembly URIs and >> has either committed to maintaining that namespace or has delegated >> maintenance of the http://www.ncbi.nlm.nih.gov/genome/ namespace to DAS. >> (If the latter is true, it is unclear which organization would receive >> such a delegation of maintenance responsibility---the Open >> Bioinformatics Foundation? The BioTeam?) >> >> Thanks for any clarifications---this question is raised solely out of a >> desire for long-term standards that can be use consistently by the >> community. >> >> Garret >> _______________________________________________ >> DAS2 mailing list >> DAS2 at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das2 >> > > > ------------------------------------------------------------ > > 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 garret at globalmentor.com Thu Mar 6 22:12:49 2008 From: garret at globalmentor.com (Garret Wilson) Date: Thu, 06 Mar 2008 14:12:49 -0800 Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces In-Reply-To: <95FDFF32-65BC-461E-A3D1-686992F865D1@fruitfly.org> References: <95FDFF32-65BC-461E-A3D1-686992F865D1@fruitfly.org> Message-ID: <47D06C61.7050805@globalmentor.com> Chris, Chris Mungall wrote: >> This issue harkens back to the URL-vs-URN-as-URI debate and whether URIs >> should be opaque, for example: >> http://rest.blueoxen.net/cgi-bin/wiki.pl?RestAndUriOpacity > > The debate has been raging on and off on various semantic web mail > lists over the years as well. Particularly the public-semweb-lifesci list Yes, I've watched those debates as well. But that's a debate that has nothing to do with the issue I raised here. > >> DAS has been designed with RESTful principles, so the abstractness >> requirement of the global seq IDs may seem unexpected. > > The consensus within the URL camp is that URLs should resolvable. I've even participated in this debate, arguing with a Nokia representative in the RDF community over whether HTTP URLs should be used for non-retrievable resources. But that's also completely ancillary to the point I raised. The point I raise here has to do with the legitimacy of using URIs in namespaces managed by third parties for a specification meant for global interoperability. It has nothing to do with opacity or resolvability of URIs. Garret From cjm at fruitfly.org Thu Mar 6 22:02:18 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Thu, 6 Mar 2008 14:02:18 -0800 Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces In-Reply-To: References: Message-ID: <95FDFF32-65BC-461E-A3D1-686992F865D1@fruitfly.org> On Mar 6, 2008, at 12:21 PM, Steve Chervitz wrote: > Hi Garret, > > As mentioned on the GlobalSeqIDs page: > > "The URLs do not need to be resolvable. At this point they are > abstract > identifiers." > > So they just happen to use ncbi, flybase, wormbase, etc. servers. > In one > sense, it doesn't matter what they are so long as all DAS servers that > provide data for these assemblies consistently use them. > > To my knowledge, none of these organizations know that we are using > their > URI namespace in this way (except maybe for wormbase, which Lincoln > -- who > came up with these IDs -- works with). Is this a weakness? Perhaps. > It's > more a sign of the fact that most organizations are not yet clued > into DAS. > > This issue harkens back to the URL-vs-URN-as-URI debate and whether > URIs > should be opaque, for example: > http://rest.blueoxen.net/cgi-bin/wiki.pl?RestAndUriOpacity The debate has been raging on and off on various semantic web mail lists over the years as well. Particularly the public-semweb-lifesci list The consensus appears to be URLs over non-URL URIs (though consensus is not necessarily right), though Mark W (guessing you're on this list Mark?) and others favour LSIDs. > DAS has been designed with RESTful principles, so the abstractness > requirement of the global seq IDs may seem unexpected. The consensus within the URL camp is that URLs should resolvable. So the DAS/2 approach of using URLs for which it would be difficult to guarantee resolvability would appear to be out of step with both camps. > I can see some advantages of using the biodas.org namespace for these > identifiers. The DAS maintainers would then be in control of > managing any > potential resolvability requirements. > But given that we've already published these global seq IDs, I > don't know > the best route to change them should we decide to do so. If we > published > biodas.org-based URIs as synonyms to the current IDs, existing DAS/ > 2 servers > and clients (of which there aren't many yet) would need to be > updated as > well, to know that http://www.ncbi.nlm.nih.gov/genome/H_sapiens/ > B33/ is > equivalent to http://biodas.org/genome/H_sapiens/B33/, for example. My feeling is that officially granted identifiers such as NC_000001.9 (current build of H_sapiens chr1) should be used where possible, with URIs constructed using some external registry of databases; eg http://www.geneontology.org/cgi-bin/xrefs.cgi However, there is clearly a need for a RESTful way of referring to sequence assemblies keyed by organism, build and chromosome, along the lines mentioned above. This could be a useful service of biodas.org I'm not sure if some notion of URI synonyms is built into DAS/2. This could perhaps be done externally via URL redirects and/or RDF metadata > Anyone else have thoughs/suggestions? > > Steve > >> From: Garret Wilson >> Organization: GlobalMentor, Inc. >> Date: Fri, 29 Feb 2008 10:31:12 -0800 >> To: >> Subject: [DAS2] approval and maintenance of DAS/2 URI namespaces >> >> I read the "list of global identifiers based on community >> consensus" at: >> >> http://www.biodas.org/wiki/GlobalSeqIDs >> >> It's great the DAS/2 is using URIs for global identification. For >> example, chromosome 1 for the B36.1 human genome assembly is >> identified >> by the URI: >> >> http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B36.1/dna/chr1 >> >> I'm unclear, however, regarding NCBI knowledge, participation, and >> maintenance of these URIs. The system of uniform resource identifiers >> prevents name clashes by delegating to the IANA-governed domain-name >> system, so that whoever owns a particular domain-based namespace can >> manage the URIs within that namespace. >> >> If DAS/2 were to use, for example, the http://www.biodas.org/genome/ >> namespace to manage all genome assembly URIs, I would have no >> cause for >> concern. DAS/2 is instead using several namespaces managed by other >> parties. I hope the response is that the NCBI is fully aware that its >> URI namespace is being used as authoritative genome assembly URIs and >> has either committed to maintaining that namespace or has delegated >> maintenance of the http://www.ncbi.nlm.nih.gov/genome/ namespace >> to DAS. >> (If the latter is true, it is unclear which organization would >> receive >> such a delegation of maintenance responsibility---the Open >> Bioinformatics Foundation? The BioTeam?) >> >> Thanks for any clarifications---this question is raised solely out >> of a >> desire for long-term standards that can be use consistently by the >> community. >> >> Garret >> _______________________________________________ >> DAS2 mailing list >> DAS2 at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das2 > > > ------------------------------------------------------------ > > 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 Fri Mar 21 19:48:56 2008 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Fri, 21 Mar 2008 12:48:56 -0700 Subject: [DAS2] BOSC 2008 Announcement and Call For Submissions Message-ID: [Sent on behalf of Darin London ] BOSC 2008 Call for Abstracts 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). The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. Many Open Source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation and dissemination of new computational methods as well as informatics infrastructure. Since the work of the Open Source Bioinformatics Community represents some of the most cutting edge of Bioinformatics in general, the overall theme for the conference this year is "Tackling Hard Problems with Emerging Technologies". Topics under this umbrella include cyberinfrastructure, grid computing and workflow management and discovery, and visualization. We will also have a s! eries of update talks about the main Open Source Bioinformatics Software suites. One of the hallmarks of BOSC is the coming together of the open source developer community in one location. A face-to-face meeting of this community creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done. This year, BOSC is accepting abstract submissions on the conference theme "Tackling Hard Problems with Emerging Technologies". The conference theme reflects that there are new technologies emerging on both the scientific front (new sequencing technologies, etc.) and the IT front (workflows, mashup/web 2.0, improvements in all of the major programming languages, etc.), which may allow the open source community to solve problems that were previously intractable. Abstracts may be submitted for the following topics. 1. Cyberinfrastructure - We are interested in presentations on topics dealing with the development of infrastructure on the web to facilitate software and data re-use (mashups, or traditional), interoperability and inter-process communication, system/service discovery, and data movement and modeling in distributed systems. This may include peer-to-peer systems of data transfer, Web Services, various flavors of data representation (SOAP, JSON, XML, others), and technologies commonly referred to under the Web 2.0 paradigm (e.g. folksonomies/tagging, user-based content generation, content feeds, and Social Networking). 2. Grid Computing and Workflow Management and Discovery - We particularly invite talks that report progress in making workflow systems easier to use and on how to do distributed-collaborative research , e.g. workflows that encompass the coordination of systems running in different parts of the world. 3. Visualization - Visualization is a maturing area of open source software development. We particularly invite talks that demonstrate innovative visualization systems in the context of workflows. 4. Open Source Software - Speakers will present talks on the use, development, or philosophy of open source software in bioinformatics. 5. Bio* Open Source Project Updates - We invite abstracts from the representatives of the open source projects sponsored by or affiliated to the O|B|F (see Projects). Please consult the official BOSC 2008 website at http://www.open-bio.org/wiki/Upcoming_BOSC_conference for all updates and extra information. 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 ------------------------------------------------------------ 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 Thu Mar 27 01:24:18 2008 From: Steve_Chervitz at affymetrix.com (Steve Chervitz) Date: Wed, 26 Mar 2008 18:24:18 -0700 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: <51CB8D74-3F41-4AD1-B4DC-F99A459C4E19@sanger.ac.uk> Message-ID: 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 From ap3 at sanger.ac.uk Thu Mar 27 13:35:26 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Thu, 27 Mar 2008 13:35:26 +0000 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: References: Message-ID: 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. From aloraine at gmail.com Thu Mar 27 14:04:21 2008 From: aloraine at gmail.com (Ann Loraine) Date: Thu, 27 Mar 2008 10:04:21 -0400 Subject: [DAS2] [DAS] DAS workshop presentations In-Reply-To: References: