From st3 at sanger.ac.uk Tue Oct 9 16:24:19 2012 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Tue, 09 Oct 2012 16:24:19 +0100 Subject: [ensembl-announce] Ensembl downtime Sun 14th Oct Message-ID: <507441A3.9020900@sanger.ac.uk> All Sanger located Ensembl based websites (www.ensembl.org, pre.ensembl.org, archives and vega.sanger.ac.uk) will be unavailable for about an hour on Sun, 14th Oct from 2030 GMT. Ensembl mirrors (useast.ensembl.org, uswest.ensembl.org and asia.ensembl.org) will continue to operate, but note that user logins from these will not be available during this period. Apologies for the inconvenience this might cause. Regards, Steve From st3 at sanger.ac.uk Mon Oct 15 15:51:09 2012 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Mon, 15 Oct 2012 15:51:09 +0100 Subject: [ensembl-announce] urgent maintenance on ensembl systems Tue 16th Oct Message-ID: <507C22DD.7030302@sanger.ac.uk> Apologies for the very short notice, but all Sanger located Ensembl based websites (www.ensembl.org, pre.ensembl.org, archives and vega.sanger.ac.uk) will be unavailable for about an hour on Tue, 16th Oct from 0800 GMT to allow urgent maintenance on underlying systems. Ensembl mirrors (useast.ensembl.org, uswest.ensembl.org and asia.ensembl.org) will continue to operate, but user logins from these will not be available during this period. There will also be a disruption tomorrow to BLAST/BLAT for about an hour between 1500 and 1600 GMT - this will affect both the main Ensembl Site and the mirrors. Apologies for the inconvenience this may cause. Regards, Steve From maurel at ebi.ac.uk Fri Oct 19 17:06:36 2012 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Fri, 19 Oct 2012 17:06:36 +0100 Subject: [ensembl-announce] Ensembl release 69 is out! Message-ID: <4C243409-2905-4750-83A5-2BFE56DB30C8@ebi.ac.uk> The latest Ensembl update (e!69) has been released : http://www.ensembl.org/ Here are some highlights: Human : Human dbSNP has been updated to release 137 and Human somatic variants from COSMIC have been updated to release 60. We now provide the 1000 genomes phase 1 data for the structural variation set, as well as DNA methylation data and ENCODE data. New species : Ferret (Mustela putorius furo) and Platyfish (Xiphophorus maculatus). Other news: We are happy to introduce the first inclusion of HAVANA manual curation for Ensembl genes in Pig, the release of the new scrollable region views and a new species home page redesign. A complete list of the changes in release 69 can be found at http://www.ensembl.org/info/website/news.html For the latest news on the ensembl project visit our blog at http://www.ensembl.info/ The release blog post can be viewed here : http://www.ensembl.info/blog/2012/10/19/ensembl-69-has-been-released/ Best Regards, Thomas Maurel -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton Cambridge - CB10 1SD - UK -------------- next part -------------- An HTML attachment was scrubbed... URL: From st3 at sanger.ac.uk Wed Oct 24 16:38:34 2012 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Wed, 24 Oct 2012 16:38:34 +0100 Subject: [ensembl-announce] Ensembl archives - short downtime Thur 25th Oct Message-ID: <50880B7A.7060909@sanger.ac.uk> The Ensembl archives will be going down for a short while tomorrow whilst we perform some hardware upgrades. Please consider the period between 1130 and 1230 GMT as 'at risk'. www.ensembl,org, mirrors, ensembldb.ensembl.org, etc will be unaffected. Apologies for any inconvenience caused. Steve From denise at ebi.ac.uk Tue Oct 30 14:55:56 2012 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Tue, 30 Oct 2012 14:55:56 +0000 Subject: [ensembl-announce] Ensembl Genomes 16 has been released! Message-ID: Dear all, The Ensembl Genomes Project is pleased to announce release 16 of Ensembl Genomes. In this release, new species include Hordeum vulgare (barley), Solanum tuberosum (potato) and Musa acuminata (banana) in Ensembl Plants; and Nasonia vitripennis (the jewel wasp) and Anopheles darlingi (Central and South American malaria mosquito) in Ensembl Metazoa. Improvements on the wheat assembly and the ability to highlight annotations in gene trees have also been released. Barley is among the world?s earliest domesticated crop species, is the fourth most abundant cereal worldwide and is a traditional model for plant genetic research. It has a large diploid genome of about 5.1Gb in size. A draft genome sequence containing the majority of barley genes and integrated with the physical map has been recently published in Nature. The genome is now available in Ensembl Plants. We have improved the alignment of a draft wheat assembly to Brachypodium distachyon and updated our presentation of wheat homoeologous SNPs using theBrachypodium reference. Significant milestones of this release are: * Ensembl Genomes displays the inferred evolutionary history of gene families in gene trees. Branches sharing specific annotation terms can now be highlighted indicating the evolution of gene function (view example) . * Ensembl Plants updates: Three new genomes: Hordeum vulgare (barley), Solanum tuberosum (potato) and Musa acuminata (banana) New EST alignments for Physcomitrella patens (moss) New repeats feature annotation for Selaginella moellendorffii (lycopod) Updated gene models for Glycine max (soybean) Updated peptide comparative genomics * Ensembl Metazoa updates: Two new species: Nasonia vitripennis (the jewel wasp) and Anopheles darlingi (Central and South American malaria mosquito), New variation dataset for Anopheles gambiae (from the insecticide resistance study at the Liverpool School of Tropical Medicine) and use of LD and transcript displays for A. gambiae variation data, Updated Pristionchus pacificus cross-references, Updated Caenorhabditis brenneri, Caenorhabditis japonica and Caenorhabditis remanei gene models and assembly, Update Drosophila melanogaster to FlyBase 5.46 including the gene models and variation consequences. * Ensembl Fungi updates: Addition of Fusarium oxysporum variation database based on sequencing of 27 different strains from the ENA Sequence Read Archive, Updated data in Puccinia graminis, Descriptions and gene names were imported from the Broad Institute, Missing InterPro annotations were added, ncRNA stable identifiers were updated, repeat features to Botryotinia fuckeliana. * Ensembl Protists updates: repeat features added for Albugo laibachii, protein features updated for all species. * Update of pan homology comparative genomics database to include latest versions of genomes from Ensembl and Ensembl Genomes * Updated BioMarts * Software migration to Ensembl 69 The Ensembl Genomes Tea -------------- next part -------------- An HTML attachment was scrubbed... URL: From st3 at sanger.ac.uk Tue Oct 9 16:24:19 2012 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Tue, 09 Oct 2012 16:24:19 +0100 Subject: [ensembl-announce] Ensembl downtime Sun 14th Oct Message-ID: <507441A3.9020900@sanger.ac.uk> All Sanger located Ensembl based websites (www.ensembl.org, pre.ensembl.org, archives and vega.sanger.ac.uk) will be unavailable for about an hour on Sun, 14th Oct from 2030 GMT. Ensembl mirrors (useast.ensembl.org, uswest.ensembl.org and asia.ensembl.org) will continue to operate, but note that user logins from these will not be available during this period. Apologies for the inconvenience this might cause. Regards, Steve From st3 at sanger.ac.uk Mon Oct 15 15:51:09 2012 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Mon, 15 Oct 2012 15:51:09 +0100 Subject: [ensembl-announce] urgent maintenance on ensembl systems Tue 16th Oct Message-ID: <507C22DD.7030302@sanger.ac.uk> Apologies for the very short notice, but all Sanger located Ensembl based websites (www.ensembl.org, pre.ensembl.org, archives and vega.sanger.ac.uk) will be unavailable for about an hour on Tue, 16th Oct from 0800 GMT to allow urgent maintenance on underlying systems. Ensembl mirrors (useast.ensembl.org, uswest.ensembl.org and asia.ensembl.org) will continue to operate, but user logins from these will not be available during this period. There will also be a disruption tomorrow to BLAST/BLAT for about an hour between 1500 and 1600 GMT - this will affect both the main Ensembl Site and the mirrors. Apologies for the inconvenience this may cause. Regards, Steve From maurel at ebi.ac.uk Fri Oct 19 17:06:36 2012 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Fri, 19 Oct 2012 17:06:36 +0100 Subject: [ensembl-announce] Ensembl release 69 is out! Message-ID: <4C243409-2905-4750-83A5-2BFE56DB30C8@ebi.ac.uk> The latest Ensembl update (e!69) has been released : http://www.ensembl.org/ Here are some highlights: Human : Human dbSNP has been updated to release 137 and Human somatic variants from COSMIC have been updated to release 60. We now provide the 1000 genomes phase 1 data for the structural variation set, as well as DNA methylation data and ENCODE data. New species : Ferret (Mustela putorius furo) and Platyfish (Xiphophorus maculatus). Other news: We are happy to introduce the first inclusion of HAVANA manual curation for Ensembl genes in Pig, the release of the new scrollable region views and a new species home page redesign. A complete list of the changes in release 69 can be found at http://www.ensembl.org/info/website/news.html For the latest news on the ensembl project visit our blog at http://www.ensembl.info/ The release blog post can be viewed here : http://www.ensembl.info/blog/2012/10/19/ensembl-69-has-been-released/ Best Regards, Thomas Maurel -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton Cambridge - CB10 1SD - UK -------------- next part -------------- An HTML attachment was scrubbed... URL: From st3 at sanger.ac.uk Wed Oct 24 16:38:34 2012 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Wed, 24 Oct 2012 16:38:34 +0100 Subject: [ensembl-announce] Ensembl archives - short downtime Thur 25th Oct Message-ID: <50880B7A.7060909@sanger.ac.uk> The Ensembl archives will be going down for a short while tomorrow whilst we perform some hardware upgrades. Please consider the period between 1130 and 1230 GMT as 'at risk'. www.ensembl,org, mirrors, ensembldb.ensembl.org, etc will be unaffected. Apologies for any inconvenience caused. Steve From denise at ebi.ac.uk Tue Oct 30 14:55:56 2012 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Tue, 30 Oct 2012 14:55:56 +0000 Subject: [ensembl-announce] Ensembl Genomes 16 has been released! Message-ID: Dear all, The Ensembl Genomes Project is pleased to announce release 16 of Ensembl Genomes. In this release, new species include Hordeum vulgare (barley), Solanum tuberosum (potato) and Musa acuminata (banana) in Ensembl Plants; and Nasonia vitripennis (the jewel wasp) and Anopheles darlingi (Central and South American malaria mosquito) in Ensembl Metazoa. Improvements on the wheat assembly and the ability to highlight annotations in gene trees have also been released. Barley is among the world?s earliest domesticated crop species, is the fourth most abundant cereal worldwide and is a traditional model for plant genetic research. It has a large diploid genome of about 5.1Gb in size. A draft genome sequence containing the majority of barley genes and integrated with the physical map has been recently published in Nature. The genome is now available in Ensembl Plants. We have improved the alignment of a draft wheat assembly to Brachypodium distachyon and updated our presentation of wheat homoeologous SNPs using theBrachypodium reference. Significant milestones of this release are: * Ensembl Genomes displays the inferred evolutionary history of gene families in gene trees. Branches sharing specific annotation terms can now be highlighted indicating the evolution of gene function (view example) . * Ensembl Plants updates: Three new genomes: Hordeum vulgare (barley), Solanum tuberosum (potato) and Musa acuminata (banana) New EST alignments for Physcomitrella patens (moss) New repeats feature annotation for Selaginella moellendorffii (lycopod) Updated gene models for Glycine max (soybean) Updated peptide comparative genomics * Ensembl Metazoa updates: Two new species: Nasonia vitripennis (the jewel wasp) and Anopheles darlingi (Central and South American malaria mosquito), New variation dataset for Anopheles gambiae (from the insecticide resistance study at the Liverpool School of Tropical Medicine) and use of LD and transcript displays for A. gambiae variation data, Updated Pristionchus pacificus cross-references, Updated Caenorhabditis brenneri, Caenorhabditis japonica and Caenorhabditis remanei gene models and assembly, Update Drosophila melanogaster to FlyBase 5.46 including the gene models and variation consequences. * Ensembl Fungi updates: Addition of Fusarium oxysporum variation database based on sequencing of 27 different strains from the ENA Sequence Read Archive, Updated data in Puccinia graminis, Descriptions and gene names were imported from the Broad Institute, Missing InterPro annotations were added, ncRNA stable identifiers were updated, repeat features to Botryotinia fuckeliana. * Ensembl Protists updates: repeat features added for Albugo laibachii, protein features updated for all species. * Update of pan homology comparative genomics database to include latest versions of genomes from Ensembl and Ensembl Genomes * Updated BioMarts * Software migration to Ensembl 69 The Ensembl Genomes Tea -------------- next part -------------- An HTML attachment was scrubbed... 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