From jw12 at sanger.ac.uk Mon Mar 8 09:16:09 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 8 Mar 2010 14:16:09 +0000 Subject: [DAS] DAS developer position at Sanger Message-ID: Senior Ensembl Web Developer DAS Support Wellcome Trust Sanger Institute Ref: 80584 Salary from ?27316 to ?37690 pa dependent on experience The Wellcome Trust Sanger Institute is a world leader in genomic research, with an expanding scientific programme dedicated to understanding gene function in health & disease. We are seeking a highly motivated senior Perl web developer with XML web services experience to develop and maintain DAS infrastructure for the Ensembl project, along with developing intuitive web displays for DAS data. The position is in the Ensembl web team working on the Ensembl sites (http://www.ensembl.org/ ). The scope of the role includes all aspects of DAS technology from client and server development to graphical display. The role requires interactions with members of the Ensembl groups based at the Wellcome Trust Sanger Institute (WTSI) and the European Bioinformatics Institute (EBI), the WTSI web team and the external DAS community. Essential Skills In order to fulfil this role you will: require a high level of competence in the Perl programming language with evidence of a high level of experience of relevant web development skills; have a scientific degree; have successfully created interfaces that link with and display data from servers delivering XML-based content into a web environment; have the communication skills required to explain complex information in simple terms to a diverse audience. Ideal Skills knowledge of DAS protocols and technologies; experience and understanding of genomic scale bioinformatics; have an ability to use productively the MySQL relational database; experience working in a Unix/Linux environment. Other information The WTSI is a world leader in genome sequencing and bioinformatics. The Ensembl project (http://www.ensembl.org/) is a collaboration between the WTSI and the EBI and provides to the scientific community annotation for approximately 50 genomes. Ensembl is the largest user of DAS technology worldwide, both for providing our annotation data and displaying data from external servers. The service we provide is used by thousands of scientists worldwide to help in their research. This position is for a fixed term of 18 months. Benefits Salary range ?27316 to ?37690 pa dependent on experience The Institute has excellent purpose built facilities on the Genome Campus, Hinxton on the outskirts of Cambridge. We offer a comprehensive range of benefits including a final salary pension scheme and excellent on-site facilities. Further details can be found on our website https://jobs.sanger.ac.uk, To submit your CV and apply for this job please go to https://jobs.sanger.ac.uk , to register and apply on line. The closing date for applications is 26 March 2010 Jonathan Warren Senior Developer and DAS coordinator -- 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 jeedward at yahoo.com Mon Mar 8 10:48:50 2010 From: jeedward at yahoo.com (John Edward) Date: Mon, 8 Mar 2010 07:48:50 -0800 (PST) Subject: [DAS] Call for papers: BCBGC-10, USA, July 2010 Message-ID: <385408.64023.qm@web45903.mail.sp1.yahoo.com> It would be highly appreciated if you could share this announcement with your colleagues, students and individuals whose research is in bioinformatics, computational biology, genomics, data-mining, and related areas. Call for papers: BCBGC-10, USA, July 2010 The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org ) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields. The following conferences are planned to be organized as part of MULTICONF-10. ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) ? International Conference on Automation, Robotics and Control Systems (ARCS-10) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) ? International Conference on Computer Communications and Networks (CCN-10) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) ? International Conference on High Performance Computing Systems (HPCS-10) ? International Conference on Information Security and Privacy (ISP-10) ? International Conference on Image and Video Processing and Computer Vision (IVPCV-10) ? International Conference on Software Engineering Theory and Practice (SETP-10) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) MULTICONF-10 will be held at Imperial Swan Hotel and Suites. It is a full-service resort that puts you in the middle of the fun! Located 1/2 block south of the famed International Drive, the hotel is just minutes from great entertainment like Walt Disney World? Resort, Universal Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and on-site dining ? all situated on 10 tropically landscaped acres. Here, guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely John Edward From jw12 at sanger.ac.uk Tue Mar 16 13:05:53 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Tue, 16 Mar 2010 17:05:53 +0000 Subject: [DAS] Chance for non-workshop attendees Message-ID: <2E08575D-2871-41D0-B4CA-B015E75F508C@sanger.ac.uk> The DAS workshop is being held in 3 weeks time. As a chance for people not attending to put their opinions forward I thought I would email the current list of suggestions for Day 3 topics. This also should give the chance for attendees to consider topics before the event so they may have more informed opinions. The list of suggested topics is below. Those who suggested the topic may or may not want to flush them out with some more details to the list ? A big topic looks to be alternative content to xml to enable faster transfer of data ( I would like for us to come up with some strategy for implementing this at the workshop). Content negotiation and efficient data formats how / if the big amounts data can be served via das DAS for high-density quantitative data. Google Proto Buffers? 1: From molecules to sets. 2: Other dimensions: Samples. Writing a DAS client in C Running DAS on amazon or google app engine. And seeing what changes have to be made to the dazzle code to enable this. I'd favour app engine. Jonathan Warren Senior Developer and DAS coordinator - Sanger -- 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 jw12 at sanger.ac.uk Fri Mar 19 08:04:36 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Fri, 19 Mar 2010 12:04:36 +0000 Subject: [DAS] 1.6 sources now in main listings Message-ID: <0B163328-CE92-48FA-B660-F41F2FBC612E@sanger.ac.uk> Taken from the http://www.dasregistry.org/ news section: 1.6 specification sources are now listed in the main lists from the registry in preparation for new 1.6 sources being created March 19, 2010 As the experimental period for DAS 1.6 is now nearing it's end, we expect the 1.6 specification to become official at this years workshop in April. Thus we are adding 1.6 sources to the list of sources at http://www.dasregistry.org/listServices.jsp and the das command http://www.dasregistry.org/das1/sources for other commands now available for listing sources please see documentation here Registrations closed for DAS workshop 2010. Jonathan Warren Senior Developer and DAS coordinator -Sanger j -- 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 jeedward at yahoo.com Thu Mar 25 10:15:32 2010 From: jeedward at yahoo.com (John Edward) Date: Thu, 25 Mar 2010 07:15:32 -0700 (PDT) Subject: [DAS] Call for papers (Deadline Extended): BCBGC-10, USA, July 2010 Message-ID: <509848.53476.qm@web45905.mail.sp1.yahoo.com> It would be highly appreciated if you could share this announcement with your colleagues, students and individuals whose research is in bioinformatics, computational biology, genomics, data-mining, and related areas. Call for papers (Deadline Extended): BCBGC-10, USA, July 2010 The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org ) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields. The following conferences are planned to be organized as part of MULTICONF-10. ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) ? International Conference on Automation, Robotics and Control Systems (ARCS-10) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) ? International Conference on Computer Communications and Networks (CCN-10) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) ? International Conference on High Performance Computing Systems (HPCS-10) ? International Conference on Information Security and Privacy (ISP-10) ? International Conference on Image and Video Processing and Computer Vision (IVPCV-10) ? International Conference on Software Engineering Theory and Practice (SETP-10) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) MULTICONF-10 will be held at Imperial Swan Hotel and Suites. It is a full-service resort that puts you in the middle of the fun! Located 1/2 block south of the famed International Drive, the hotel is just minutes from great entertainment like Walt Disney World? Resort, Universal Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and on-site dining ? all situated on 10 tropically landscaped acres. Here, guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely John Edward From jw12 at sanger.ac.uk Mon Mar 8 14:16:09 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 8 Mar 2010 14:16:09 +0000 Subject: [DAS] DAS developer position at Sanger Message-ID: Senior Ensembl Web Developer DAS Support Wellcome Trust Sanger Institute Ref: 80584 Salary from ?27316 to ?37690 pa dependent on experience The Wellcome Trust Sanger Institute is a world leader in genomic research, with an expanding scientific programme dedicated to understanding gene function in health & disease. We are seeking a highly motivated senior Perl web developer with XML web services experience to develop and maintain DAS infrastructure for the Ensembl project, along with developing intuitive web displays for DAS data. The position is in the Ensembl web team working on the Ensembl sites (http://www.ensembl.org/ ). The scope of the role includes all aspects of DAS technology from client and server development to graphical display. The role requires interactions with members of the Ensembl groups based at the Wellcome Trust Sanger Institute (WTSI) and the European Bioinformatics Institute (EBI), the WTSI web team and the external DAS community. Essential Skills In order to fulfil this role you will: require a high level of competence in the Perl programming language with evidence of a high level of experience of relevant web development skills; have a scientific degree; have successfully created interfaces that link with and display data from servers delivering XML-based content into a web environment; have the communication skills required to explain complex information in simple terms to a diverse audience. Ideal Skills knowledge of DAS protocols and technologies; experience and understanding of genomic scale bioinformatics; have an ability to use productively the MySQL relational database; experience working in a Unix/Linux environment. Other information The WTSI is a world leader in genome sequencing and bioinformatics. The Ensembl project (http://www.ensembl.org/) is a collaboration between the WTSI and the EBI and provides to the scientific community annotation for approximately 50 genomes. Ensembl is the largest user of DAS technology worldwide, both for providing our annotation data and displaying data from external servers. The service we provide is used by thousands of scientists worldwide to help in their research. This position is for a fixed term of 18 months. Benefits Salary range ?27316 to ?37690 pa dependent on experience The Institute has excellent purpose built facilities on the Genome Campus, Hinxton on the outskirts of Cambridge. We offer a comprehensive range of benefits including a final salary pension scheme and excellent on-site facilities. Further details can be found on our website https://jobs.sanger.ac.uk, To submit your CV and apply for this job please go to https://jobs.sanger.ac.uk , to register and apply on line. The closing date for applications is 26 March 2010 Jonathan Warren Senior Developer and DAS coordinator -- 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 jeedward at yahoo.com Mon Mar 8 15:48:50 2010 From: jeedward at yahoo.com (John Edward) Date: Mon, 8 Mar 2010 07:48:50 -0800 (PST) Subject: [DAS] Call for papers: BCBGC-10, USA, July 2010 Message-ID: <385408.64023.qm@web45903.mail.sp1.yahoo.com> It would be highly appreciated if you could share this announcement with your colleagues, students and individuals whose research is in bioinformatics, computational biology, genomics, data-mining, and related areas. Call for papers: BCBGC-10, USA, July 2010 The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org ) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields. The following conferences are planned to be organized as part of MULTICONF-10. ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) ? International Conference on Automation, Robotics and Control Systems (ARCS-10) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) ? International Conference on Computer Communications and Networks (CCN-10) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) ? International Conference on High Performance Computing Systems (HPCS-10) ? International Conference on Information Security and Privacy (ISP-10) ? International Conference on Image and Video Processing and Computer Vision (IVPCV-10) ? International Conference on Software Engineering Theory and Practice (SETP-10) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) MULTICONF-10 will be held at Imperial Swan Hotel and Suites. It is a full-service resort that puts you in the middle of the fun! Located 1/2 block south of the famed International Drive, the hotel is just minutes from great entertainment like Walt Disney World? Resort, Universal Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and on-site dining ? all situated on 10 tropically landscaped acres. Here, guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely John Edward From jw12 at sanger.ac.uk Tue Mar 16 17:05:53 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Tue, 16 Mar 2010 17:05:53 +0000 Subject: [DAS] Chance for non-workshop attendees Message-ID: <2E08575D-2871-41D0-B4CA-B015E75F508C@sanger.ac.uk> The DAS workshop is being held in 3 weeks time. As a chance for people not attending to put their opinions forward I thought I would email the current list of suggestions for Day 3 topics. This also should give the chance for attendees to consider topics before the event so they may have more informed opinions. The list of suggested topics is below. Those who suggested the topic may or may not want to flush them out with some more details to the list ? A big topic looks to be alternative content to xml to enable faster transfer of data ( I would like for us to come up with some strategy for implementing this at the workshop). Content negotiation and efficient data formats how / if the big amounts data can be served via das DAS for high-density quantitative data. Google Proto Buffers? 1: From molecules to sets. 2: Other dimensions: Samples. Writing a DAS client in C Running DAS on amazon or google app engine. And seeing what changes have to be made to the dazzle code to enable this. I'd favour app engine. Jonathan Warren Senior Developer and DAS coordinator - Sanger -- 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 jw12 at sanger.ac.uk Fri Mar 19 12:04:36 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Fri, 19 Mar 2010 12:04:36 +0000 Subject: [DAS] 1.6 sources now in main listings Message-ID: <0B163328-CE92-48FA-B660-F41F2FBC612E@sanger.ac.uk> Taken from the http://www.dasregistry.org/ news section: 1.6 specification sources are now listed in the main lists from the registry in preparation for new 1.6 sources being created March 19, 2010 As the experimental period for DAS 1.6 is now nearing it's end, we expect the 1.6 specification to become official at this years workshop in April. Thus we are adding 1.6 sources to the list of sources at http://www.dasregistry.org/listServices.jsp and the das command http://www.dasregistry.org/das1/sources for other commands now available for listing sources please see documentation here Registrations closed for DAS workshop 2010. Jonathan Warren Senior Developer and DAS coordinator -Sanger j -- 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 jeedward at yahoo.com Thu Mar 25 14:15:32 2010 From: jeedward at yahoo.com (John Edward) Date: Thu, 25 Mar 2010 07:15:32 -0700 (PDT) Subject: [DAS] Call for papers (Deadline Extended): BCBGC-10, USA, July 2010 Message-ID: <509848.53476.qm@web45905.mail.sp1.yahoo.com> It would be highly appreciated if you could share this announcement with your colleagues, students and individuals whose research is in bioinformatics, computational biology, genomics, data-mining, and related areas. Call for papers (Deadline Extended): BCBGC-10, USA, July 2010 The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org ) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields. The following conferences are planned to be organized as part of MULTICONF-10. ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) ? International Conference on Automation, Robotics and Control Systems (ARCS-10) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) ? International Conference on Computer Communications and Networks (CCN-10) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) ? International Conference on High Performance Computing Systems (HPCS-10) ? International Conference on Information Security and Privacy (ISP-10) ? International Conference on Image and Video Processing and Computer Vision (IVPCV-10) ? International Conference on Software Engineering Theory and Practice (SETP-10) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) MULTICONF-10 will be held at Imperial Swan Hotel and Suites. It is a full-service resort that puts you in the middle of the fun! Located 1/2 block south of the famed International Drive, the hotel is just minutes from great entertainment like Walt Disney World? Resort, Universal Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and on-site dining ? all situated on 10 tropically landscaped acres. Here, guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely John Edward