From darin.london at duke.edu Tue Mar 18 14:16:59 2008 From: darin.london at duke.edu (darin.london at duke.edu) Date: Tue, 18 Mar 2008 13:16:59 -0500 Subject: [DAS] BOSC 2008 Announcement and Call For Submissions Message-ID: <200803181816.m2IIGxlY007281@tenero.duhs.duke.edu> 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 series 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 From ap3 at sanger.ac.uk Wed Mar 26 12:01:26 2008 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Wed, 26 Mar 2008 16:01:26 +0000 Subject: [DAS] DAS workshop presentations Message-ID: <51CB8D74-3F41-4AD1-B4DC-F99A459C4E19@sanger.ac.uk> 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. 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: [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 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: [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 aloraine at gmail.com Thu Mar 27 10:04:32 2008 From: aloraine at gmail.com (Ann Loraine) Date: Thu, 27 Mar 2008 14:04:32 -0000 Subject: [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 >