From adrian.paschke at gmx.de Tue Oct 6 12:02:10 2009 From: adrian.paschke at gmx.de (Adrian Paschke) Date: Tue, 6 Oct 2009 21:02:10 +0200 Subject: [Gofriends] Deadline Oct. 12th - Semantic Web Applications and Tools for Life Sciences Message-ID: <200910061902.n96J2GqD028395@fafner.Stanford.EDU> ------------------------------------------------ Submission deadline for papers is October 12 ------------------------------------------------ SWAT4LS Semantic Web Applications and Tools for Life Sciences *** apologies for multiple postings *** --- updates --- We are glad to announce that there will be a special issue of the BMC Journal of Biomedical Semantics dedicated to the SWAT4LS workshop. This is a new open access journal published by BMC and we are confident that the supplement will benefit from the additional exposure and promotion associated with its launch (more information on this journal can be found at http://www.jbiomedsem.com/). The call for this special issue will be open to all the contributors to the SWAT4LS workshop (accepted papers, posters and demos). Authors will be invited to submit an extended version of their work, elaborated in the light of the discussion held at the workshop. Workshop proceedings will be published on CEUR. In order to facilitate submissions, we have extended submission deadlines as follows: submission of papers: October 12 submission of posters and demos: October 15 communication of acceptance: October 28 camera ready: November 13 Due to the limited time for reviews, we would ask you to submit an abstract of your paper by October 5th, in order to facilitate assignment of reviews. The lenght of contributions to the workshop as been revised to offer more flexibility: * Submissions for Oral communications should be between 8 and 15 pages. * Posters submissions should be between 2 and 4 pages. * Software demo proposals should also be between 2 and 4 pages. Finally, we would like to announce that the special issue BMC Bioinformatics dedicated to SWAT4LS-2008 will be published on October 1st (BMC Bioinformatics, Vol 10, Supp 10) --- call for papers --- ***Location and date Amsterdam, Science Park, November 20th 2009 (http://swat4ls.org/2009/) ***Rationale The adoption of semantic-enabled applications and collaborative social environments is ever more common in the Life Sciences. The Semantic Web provides a set of technologies and standards that are key to support semantic markup, ontology development, distributed information resources and collaborative social environments. Altogether the adoption of the Semantic Web in the Life Sciences has potential impact on the future of publishing, biological research and medecine. This workshop will provide a venue to present and discuss benefits and limits of the adoption of these technologies and tools in biomedical informatics and computational biology. It will showcase experiences, information resources, tools development and applications. It will bring together researchers, both developers and users, from the various fields of Biology, Bioinformatics and Computer Science, to discuss goals, current limits and some real use cases for Semantic Web technologies in Life Sciences. ***Topics Topics of interest include, but are not limited to: * Standards, Technologies, Tools for the Semantic Web o Semantic Web standards and new proposals (RDF, OWL, SKOS,... ) o Biomedical Ontologies and related tools o Formal approaches to large biomedical knowledge bases * Systems for a Semantic Web for Bioinformatics o RDF stores, Reasoners, query and visualization systems for life sciences o Semantic biomedical Web Services o Semantics aware Biological Data Integration Systems * Existing and prospective applications of the Semantic Web for Bioinformatics o Semantics aware application tools o Semantic collaborative research environments o Case studies, use cases, and scenarios ***Scientific Program The workshop will be interactive and include keynotes, oral presentations, panel discussion and a poster and demo session. The keynote speakers of this edition will be: * Barend Mons (http://www.biosemantics.org/index.php?page=barend-mons ) * Michael Schroeder (http://www.biotec.tu-dresden.de/schroeder) * Alan Ruttenberg (http://sciencecommons.org/about/whoweare/ruttenberg/ ) ***Scientific Committee (committed so far:) * Christopher J. O. Baker, Department of Computer Science and Applied Statistics, University of Brunswick, Canada * Pedro Barahona, Department of Informatics, New University of Lisboa, Lisboa, Portugal * Liliana Barrio-Alvers, Transinsight GmbH, Dresden, Germany * Olivier Bodenreider, National Library of Medicine, Bethesda, MD, United States of America * Matt-Mouley Bouamrane, School of Computer Science, University of Machester, manchester, United Kingdom * Werner Ceusters, NY CoE in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, United States of America * Kei Cheung, Center for Medical Informatics, Yale University School of Medicine, New Haven, United States of America * Tim Clark, Massachusetts General Hospital and Harvard Medical School, Boston MA, United States of America * Marie-Dominique Devignes, LORIA, Vandoeuvre les Nancy, France * Olivier Dameron, INSERM U936, University of Rennes 1, France * Michel Dumontier, Carleton University, Ottawa, Ontario, Canada * Huajun Chen, Zhejiang University, China * Duncan Hull, School of Chemistry, University of Manchester, UK * C. Maria Keet, Faculty of Computer Science, Free University of Bozen-Bolzano, Bolzano, Italy * Graham Kemp, Chalmers University of Technology, Sweden * Jacob Tilman Koehler, Department of Molecular Biotechnology, Institute of Medical Biology, University of Troms?, Troms?, Norway * Michael Krauthammer, Department of Pathology, Yale University School of Medicine, United States of America * Martin Kuiper, Department of Pathology, Systems Biology group, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway * Patrick Lambrix, Department of Computer and Information Science, Link?ping University, Link?ping, Sweden * Phillip Lord, School of Computing Science, Newcastle University, Newcastle-upon-Tyne, United Kingdom * M. Scott Marshall, Leiden University Medical Center / University of Amsterdam, The Netherlands * Chris Mungall, Lawrence Berkeley National Laboratories, United States of America * Stephan Philippi, Institute for Software Technology, University of Koblenz-Landau, Koblenz, Germany * Marco Roos, Instituut voor Informatica, University of Amsterdam, Netherlands * Alan Ruttenberg, Science Commons, Cambridge, MA, United States of America * Matthias Samwald, DERI, Galway, Ireland, and Konrad Lorenz Institute for Evolution and Cognition Research, Altenberg, Austria * Nigam Shah, Center for Biomedical Informatics Research, Stanford, United States of America * Michael Schr?der, Biotechnology Centre, TU Dresden, Dresden, Germany * Robert Stevens, School of Computer Science, University of Manchester, Manchester, United Kingdom * Tetsuro Toyoda, Genomic Sciences Center, RIKEN, Yokohama, Japan * Mark D. Wilkinson, iCAPTURE Center, St. Paul Hospital, Vancouver, Canada and the organizers ***Type of contributions The following possible contributions are sought: * Oral communications (regular papers) * Posters * Software demos ***Proceedings All accepted oral communications and posters will be published with the CEUR-WS.org Workshop Proceedings service (see http://ceur-ws.org/). We are finalizing the agreement to have a dedicated special issue on the 2009 edition of swat4ls in an international scientific journal of the BMC group (open access, pubmed indexed). To this end, a special Call will be launched shortly after the workshop, for extended and revised versions of contributions submitted to the workshop and accepted either as oral communication or poster. ***New Deadlines * Intention to submit (abstract only): October 5th * Submission of papers: October 12 * Submission of posters and demos: October 15 * Communication of acceptance: October 28 * Camera ready: November 13 ***Instructions All papers and posters must be in English and must be submitted through the EasyChair review system at http://www.easychair.org/conferences/?conf=swat4ls-09 . Please upload all submissions as PDF files in LNCS format (http://www.springer.de/comp/lncs/authors.html ). To ensure high quality, submitted papers will be carefully peer- reviewed by at least three members of the Scientific Committee. * Submissions for Oral communications should be between 8 and 15 pages. * Posters submissions should be between 2 and 4 pages. * Software demo proposals should also be between 2 and 4 pages. ***Organization * M. Scott Marshall, Leiden University Medical Center / University of Amsterdam, The Netherlands * Albert Burger, School of Mathematical and Computer Sciences, Heriot-Watt University, and Human Genetics Unit, Medical Research Council, Edinburgh, Scotland, United Kingdom * Adrian Paschke, Corporate Semantic Web, Freie Universitaet Berlin, Germany * Paolo Romano, Bioinformatics, National Cancer Research Institute, Genova, Italy * Andrea Splendiani, Biomathematics and Bioinformatics dept., Rothamsted Research, UK ***More information * http://www.swat4ls.org/2009/ * http://swat4ls.blogspot.com * info at swat4ls.org From tonys at ebi.ac.uk Thu Oct 8 01:04:17 2009 From: tonys at ebi.ac.uk (Tony Sawford) Date: Thu, 08 Oct 2009 09:04:17 +0100 Subject: [Gofriends] GOA release [2009-10-08] Message-ID: <4ACD9D01.4010605@ebi.ac.uk> GOA releases: 08 October 2009 ============================= GOA (GO Annotation at EBI) is a project run by the European Bioinformatics Institute that provides assignments of gene products to the Gene Ontology (GO) resource. The data can be obtained via: EBI FTP: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/ EBI SRS: http://srs.ebi.ac.uk. Search GOA data library GO FTP: ftp://ftp.geneontology.org/pub/go/gene-associations/ GO CVS: http://www.geneontology.org/GO.CVS.help.html For further information read: http://www.ebi.ac.uk/GOA or contact goa at ebi.ac.uk. Please note that the contents of the gene_association.goa_pdb file has changed as of this release, as GOA is no longer able to provide annotations to specific PDB chains. In future annotations in this file will only associate PDB entries with GO terms. As an example, an annotation line in the PDB file has changed from: PDB 102M_A q_A GO:0005506 GOA:interpro IEA InterPro:IPR000971 F protein_structure taxon:9755 20090629 UniProtKB to: PDB 102M 102M GO:0005506 GOA:interpro IEA InterPro:IPR000971 F protein_structure taxon:9755 20091001 UniProtKB Please contact us if this change is of concern. Regards, GOA Production From cherry at stanford.edu Sun Oct 18 14:08:31 2009 From: cherry at stanford.edu (Mike Cherry) Date: Sun, 18 Oct 2009 14:08:31 -0700 Subject: [Gofriends] Bioinformatic Analyst position with SGD Message-ID: <7D9D1A13-A1CC-4E77-9A30-BE3C42D53C39@stanford.edu> Fixed Term Position - Application Bioinformatics Analyst, Research Stanford University's Department of Genetics has an excellent opportunity available for a motivated and experienced Bioinformatic Analyst. This individual will be an essential project member interacting with international research laboratories and taking responsibility for evaluating these data. Experience in genomic data and the ability to evaluation new technologies are needed to successfully define the use of these data. The analysis will be via computational methods created by others but integrated at SGD. Knowledge of new experimental methodology, large genomic datasets and their computational analysis is expected. The experience should include the bioinformatic analysis of data types such as RNA transcription and second-generation sequencing. Experience with comparative genomics is desirable. An advanced education in biology is required to facilitate the assessment of experimental details and to successfully evaluate quality control of novel experimental data. The successful candidate must be able to learn and work independently, yet collaborate effectively with co-workers. Previous experience working in an academic environment is a plus. The candidate will be expected to participate in group discussions regarding software specification, design, and implementation with both programming and non-programming staff at SGD. The work will take place in a dynamic environment where specifications often change rapidly in response to user demand, so the candidate must be able to be flexible in his or her software design and implementations. This position will work within the Saccharomyces Genome Database project. Compliance with all institutional and governmental health and safety regulations and policies is required. Qualifications: ? Advanced degree in Biology or Bioinformatics, plus 5 years experience. ? Experience with data quality assessment. ? Experience with relational databases and Perl scripting. ? Excellent verbal and written communication skills. ? Knowledge of modern high-throughput genomics and proteomics experiments and their data types. Desired Qualifications: ? Four-year college degree in Computer Science. ? Laboratory experience with Saccharomyces, Drosophila or Caenorhabditis. ? Experience with software development environments. ? Laboratory experience in genetics or molecular biology. ? Experience with comparative genomics is desirable. For more information or to apply see : http://jobs.stanford.edu/ job number : 36125 From markw at illuminae.com Wed Oct 28 18:11:06 2009 From: markw at illuminae.com (Mark) Date: Wed, 28 Oct 2009 18:11:06 -0700 Subject: [Gofriends] EBI Go database down? Message-ID: Hi all GO Friends! Our SADI Gene Ontology service recently went down: go_latest:mysql.ebi.ac.uk:4085 Is the DB offline or has it moved? Any advice appreciated :-) cheers all! Mark From midori at ebi.ac.uk Thu Oct 29 02:55:35 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 29 Oct 2009 09:55:35 +0000 (GMT) Subject: [Gofriends] EBI Go database down? In-Reply-To: References: Message-ID: Hello, This message from the GO software group may be relevant: > If you are maintaining a mirror and using the go-dev script: > /go-dev/go-db-perl/scripts/go_db_install.pl > > You must update to the newest version--some of the filenames have > changed and the old version will no longer work with the lite DBs. > > Cheers, > > -Seth If you are not using the go_db_install.pl script, or if updating it does not fix your problem, please let us know via the GO Helpdesk . Regards, Midori On Wed, 28 Oct 2009, Mark wrote: > Hi all GO Friends! > > Our SADI Gene Ontology service recently went down: > go_latest:mysql.ebi.ac.uk:4085 > > Is the DB offline or has it moved? > > Any advice appreciated :-) cheers all! > > Mark ============================ Midori A. Harris, Ph.D. GO Editor EMBL - EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 (0) 1223 494667 Fax: +44 (0) 1223 494468 Email: midori at ebi.ac.uk From markw at illuminae.com Thu Oct 29 08:42:19 2009 From: markw at illuminae.com (Mark) Date: Thu, 29 Oct 2009 08:42:19 -0700 Subject: [Gofriends] EBI Go database down? In-Reply-To: References: Message-ID: On Thu, 29 Oct 2009 02:55:35 -0700, Midori Harris wrote: > If you are not using the go_db_install.pl script, or if updating it does > not fix your problem, please let us know via the GO Helpdesk > . we are not using a local installation - we are connecting directly to the public EBI mySQL port.... so I don't think this solution is relevant for us. Other ideas? Mark From suzi at fruitfly.org Thu Oct 29 09:09:58 2009 From: suzi at fruitfly.org (Suzanna Lewis) Date: Thu, 29 Oct 2009 09:09:58 -0700 Subject: [Gofriends] EBI Go database down? In-Reply-To: References: Message-ID: Yes, but the EBI installation itself is a mirror. Midori or Dan, do you know if the refresh scripts at the EBI mirror have been updated? There was a bug in the last update that would cause a failure. -S On Oct 29, 2009, at 8:42 AM, Mark wrote: > On Thu, 29 Oct 2009 02:55:35 -0700, Midori Harris > wrote: > > >> If you are not using the go_db_install.pl script, or if updating it >> does >> not fix your problem, please let us know via the GO Helpdesk >> . > > > we are not using a local installation - we are connecting directly > to the public EBI mySQL port.... so I don't think this solution is > relevant for us. > > Other ideas? > > Mark > _______________________________________________ > Gofriends mailing list > Gofriends at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/gofriends > From jane at ebi.ac.uk Thu Oct 29 09:15:04 2009 From: jane at ebi.ac.uk (Jane Lomax) Date: Thu, 29 Oct 2009 16:15:04 +0000 Subject: [Gofriends] EBI Go database down? In-Reply-To: References: Message-ID: <4AE9BF88.2070903@ebi.ac.uk> Dan is on leave this week - I think Tony is trying to work this out with Seth though... Suzanna Lewis wrote: > Yes, but the EBI installation itself is a mirror. > > Midori or Dan, do you know if the refresh scripts at the EBI mirror > have been updated? There was a bug in the last update that would cause > a failure. > > -S > > On Oct 29, 2009, at 8:42 AM, Mark wrote: > >> On Thu, 29 Oct 2009 02:55:35 -0700, Midori Harris >> wrote: >> >> >>> If you are not using the go_db_install.pl script, or if updating it >>> does >>> not fix your problem, please let us know via the GO Helpdesk >>> . >> >> >> we are not using a local installation - we are connecting directly to >> the public EBI mySQL port.... so I don't think this solution is >> relevant for us. >> >> Other ideas? >> >> Mark >> _______________________________________________ >> Gofriends mailing list >> Gofriends at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/gofriends >> > > _______________________________________________ > Gofriends mailing list > Gofriends at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/gofriends -- Dr Jane Lomax GO Editorial Office EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridgeshire, UK CB10 1SD p: +44 1223 492516 f: +44 1223 494468 From suzi at fruitfly.org Thu Oct 29 09:49:14 2009 From: suzi at fruitfly.org (Suzanna Lewis) Date: Thu, 29 Oct 2009 09:49:14 -0700 Subject: [Gofriends] EBI Go database down? In-Reply-To: <4AE9BF88.2070903@ebi.ac.uk> References: <4AE9BF88.2070903@ebi.ac.uk> Message-ID: Great thanks Jane. Mark, we're also setting up other mirrors (at Berkeley, Princeton, and Northwestern). They aren't quite ready for prime time, but we'll let you know when they do go online. -S On Oct 29, 2009, at 9:15 AM, Jane Lomax wrote: > Dan is on leave this week - I think Tony is trying to work this out > with Seth though... > > Suzanna Lewis wrote: >> Yes, but the EBI installation itself is a mirror. >> >> Midori or Dan, do you know if the refresh scripts at the EBI mirror >> have been updated? There was a bug in the last update that would >> cause a failure. >> >> -S >> >> On Oct 29, 2009, at 8:42 AM, Mark wrote: >> >>> On Thu, 29 Oct 2009 02:55:35 -0700, Midori Harris >>> wrote: >>> >>> >>>> If you are not using the go_db_install.pl script, or if updating >>>> it does >>>> not fix your problem, please let us know via the GO Helpdesk >>>> . >>> >>> >>> we are not using a local installation - we are connecting directly >>> to the public EBI mySQL port.... so I don't think this solution is >>> relevant for us. >>> >>> Other ideas? >>> >>> Mark >>> _______________________________________________ >>> Gofriends mailing list >>> Gofriends at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/gofriends >>> >> >> _______________________________________________ >> Gofriends mailing list >> Gofriends at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/gofriends > > > -- > Dr Jane Lomax > GO Editorial Office > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridgeshire, UK > CB10 1SD > > p: +44 1223 492516 > f: +44 1223 494468 > > From markw at illuminae.com Thu Oct 29 10:49:07 2009 From: markw at illuminae.com (Mark) Date: Thu, 29 Oct 2009 10:49:07 -0700 Subject: [Gofriends] EBI Go database down? In-Reply-To: References: <4AE9BF88.2070903@ebi.ac.uk> Message-ID: Thanks Suzi! Mark On Thu, 29 Oct 2009 09:49:14 -0700, Suzanna Lewis wrote: > Great thanks Jane. > > Mark, we're also setting up other mirrors (at Berkeley, Princeton, and > Northwestern). They aren't quite ready for prime time, but we'll let > you know when they do go online. From tonys at ebi.ac.uk Fri Oct 30 01:01:57 2009 From: tonys at ebi.ac.uk (Tony Sawford) Date: Fri, 30 Oct 2009 08:01:57 +0000 Subject: [Gofriends] EBI Go database down? In-Reply-To: <4AE9BF88.2070903@ebi.ac.uk> References: <4AE9BF88.2070903@ebi.ac.uk> Message-ID: <4AEA9D75.7060103@ebi.ac.uk> Yes, but unfortunately it's looking like we're going to have to wait until Dan returns next week to get this sorted out. We have all the latest scripts, so I don't think that's the problem - it seems like our server just doesn't want to talk to anybody at the moment... Tony Jane Lomax wrote: > Dan is on leave this week - I think Tony is trying to work this out > with Seth though... > > Suzanna Lewis wrote: >> Yes, but the EBI installation itself is a mirror. >> >> Midori or Dan, do you know if the refresh scripts at the EBI mirror >> have been updated? There was a bug in the last update that would >> cause a failure. >> >> -S >> >> On Oct 29, 2009, at 8:42 AM, Mark wrote: >> >>> On Thu, 29 Oct 2009 02:55:35 -0700, Midori Harris >>> wrote: >>> >>> >>>> If you are not using the go_db_install.pl script, or if updating it >>>> does >>>> not fix your problem, please let us know via the GO Helpdesk >>>> . >>> >>> >>> we are not using a local installation - we are connecting directly >>> to the public EBI mySQL port.... so I don't think this solution is >>> relevant for us. >>> >>> Other ideas? >>> >>> Mark >>> _______________________________________________ >>> Gofriends mailing list >>> Gofriends at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/gofriends >>> >> >> _______________________________________________ >> Gofriends mailing list >> Gofriends at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/gofriends > >