From amonida at ebi.ac.uk Fri Mar 13 11:03:21 2015 From: amonida at ebi.ac.uk (Amonida Zadissa) Date: Fri, 13 Mar 2015 11:03:21 +0000 Subject: [ensembl-announce] Ensembl 79 is out! Message-ID: <5502C3F9.7080602@ebi.ac.uk> Hi all, We are pleased to announce that the latest Ensembl update (e!79) has been released: http://www.ensembl.org/ Highlights include: * Human: genes updated to GENCODE 22, and new assembly patches (GRCh38.p2) * Comparison of imported human RefSeq transcript set to Ensembl models * New interactive gene gain/loss tree view * Global Alliance REST endpoints * NextGen project genotype sheep data from Iranian and Moroccan populations A complete list of the changes can be found on http://www.ensembl.org/info/website/news.html. Also, for the latest news from the Ensembl project visit our blog at http://www.ensembl.info. The e79 webinar is planned for Thursday, 26 March, 16.00 GMT, please register using the following URL. Registration is free. https://attendee.gototraining.com/r/5346296490257871873 Best regards, Amonida From maurel at ebi.ac.uk Thu Mar 19 16:02:26 2015 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Thu, 19 Mar 2015 16:02:26 +0000 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 80 Message-ID: <8E00D061-1B3E-41F6-B5D5-E1C8EF9D1DA1@ebi.ac.uk> Dear all, Please find the summary of the declarations of intentions for Ensembl release 80 (scheduled for the 12th of May 2015) on our public website (http://admin.ensembl.org/Changelog/Summary ). Note these are intentions and are not guaranteed to be in the release. Regards, Thomas -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: From denise at ebi.ac.uk Wed Mar 25 11:52:07 2015 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Wed, 25 Mar 2015 11:52:07 +0000 Subject: [ensembl-announce] Ensembl Genomes release 26 is out! Message-ID: <7B68E870-E3FE-457B-AC95-9CFAB58BB2C4@ebi.ac.uk> Dear all, We are delighted to announce that the latest update of Ensembl Genomes has been released. Highlights ? Updated names and descriptions for Strigamia maritima genes ? 777 new bacterial genomes (Ensembl Bacteria now contains 21,767genomes) ? Assemblies 2.40 and 2.50 of tomato available in Assembly Converter (to transfer genomic coordinates between assemblies) ? New variation data for the plant pathogens Verticillium dahliae (JR2 strain) and Zymoseptoria tritici Genome comparisons for Triticeae and related species Whole genome alignments between seven pairs of Triticeae genomes, including the bread wheat A, B and D component genomes, Triticum urartu (the A genome progenitor), Aegilops tauschii (the D genome progenitor), and barley are now available. The alignments were obtained using ATAC and the statistics on genome and coding exon coverages can be found on our website. MAF files on our FTP sites In response to several requests from our users we now provide the pairwise alignments as MAF files. These can be found on the FTP download site of all Ensembl Genomes divisions. Other news ? Fungi and Protists: Updated PHIbase annotation and protein domain information based on InterProScan ? Latest assemblies and gene sets for Medicago truncatula and Oryza meridionalis ? New RNASeq data in barley, Oryza sp and Leersia perrieri A complete list of both new and updated date can be found on our website. Any questions or comments? Email us at helpdesk at ensemblgenomes.org The Ensembl Genomes team -------------- next part -------------- An HTML attachment was scrubbed... URL: From dstaines at ebi.ac.uk Wed Mar 25 13:35:17 2015 From: dstaines at ebi.ac.uk (Dan Staines) Date: Wed, 25 Mar 2015 13:35:17 +0000 Subject: [ensembl-announce] Ensembl Genomes public MySQL data retention Message-ID: <5512B995.9010402@ebi.ac.uk> As the amount of data in each release of Ensembl Genomes increases, it has become necessary to restrict the number of past releases available on our public MySQL server (mysql-eg-publicsql.ebi.ac.uk). Towards the end of May 2015, shortly before the release 27 of Ensembl Genomes, all databases from all releases prior to release 18 will be removed. With each subsequent release, data from the oldest release will be removed at release time, leaving data from the most recent 10 releases only. The removal of each release will be announced with the intentions for the new release approximately 2 months in advance. Please note that the data available from our FTP site will be unaffected by this change in policy, with data from all releases of Ensembl Genomes remaining available in all supported formats, including full MySQL dumps. Regards, Dan Staines, on behalf of the Ensembl Genomes team. -- Dan Staines, PhD Ensembl Genomes Technical Coordinator EMBL-EBI Tel: +44-(0)1223-492507 Wellcome Trust Genome Campus Fax: +44-(0)1223-494468 Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/ From maurel at ebi.ac.uk Tue Mar 31 15:27:08 2015 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Tue, 31 Mar 2015 15:27:08 +0100 Subject: [ensembl-announce] GRCh37 release 79 data update Message-ID: <0F253C22-7B05-45F1-AA8E-AA1996B57145@ebi.ac.uk> Dear all, We are pleased to announce that the first Ensembl data update for human GRCh37 (e!79) has been released: http://grch37.ensembl.org/index.html Highlights include: Added variation data for human from dbSNP 142 Imported Genotypes from 1000 Genomes Phase 3 New regulatory build for human Imported latest release of public HGMD data (version 2014.4) Imported COSMIC data version 71 Added RefSeq GFF3 annotation A complete list of the changes can be found on: http://grch37.ensembl.org/info/website/news.html Also, for the latest news from the Ensembl project visit our blog at http://www.ensembl.info The GRCh37 release 79 blog post can be viewed here: http://www.ensembl.info/blog/2015/03/31/first-update-of-the-ensembl-grch37-site/ Regards, Thomas -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: From amonida at ebi.ac.uk Fri Mar 13 11:03:21 2015 From: amonida at ebi.ac.uk (Amonida Zadissa) Date: Fri, 13 Mar 2015 11:03:21 +0000 Subject: [ensembl-announce] Ensembl 79 is out! Message-ID: <5502C3F9.7080602@ebi.ac.uk> Hi all, We are pleased to announce that the latest Ensembl update (e!79) has been released: http://www.ensembl.org/ Highlights include: * Human: genes updated to GENCODE 22, and new assembly patches (GRCh38.p2) * Comparison of imported human RefSeq transcript set to Ensembl models * New interactive gene gain/loss tree view * Global Alliance REST endpoints * NextGen project genotype sheep data from Iranian and Moroccan populations A complete list of the changes can be found on http://www.ensembl.org/info/website/news.html. Also, for the latest news from the Ensembl project visit our blog at http://www.ensembl.info. The e79 webinar is planned for Thursday, 26 March, 16.00 GMT, please register using the following URL. Registration is free. https://attendee.gototraining.com/r/5346296490257871873 Best regards, Amonida From maurel at ebi.ac.uk Thu Mar 19 16:02:26 2015 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Thu, 19 Mar 2015 16:02:26 +0000 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 80 Message-ID: <8E00D061-1B3E-41F6-B5D5-E1C8EF9D1DA1@ebi.ac.uk> Dear all, Please find the summary of the declarations of intentions for Ensembl release 80 (scheduled for the 12th of May 2015) on our public website (http://admin.ensembl.org/Changelog/Summary ). Note these are intentions and are not guaranteed to be in the release. Regards, Thomas -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: From denise at ebi.ac.uk Wed Mar 25 11:52:07 2015 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Wed, 25 Mar 2015 11:52:07 +0000 Subject: [ensembl-announce] Ensembl Genomes release 26 is out! Message-ID: <7B68E870-E3FE-457B-AC95-9CFAB58BB2C4@ebi.ac.uk> Dear all, We are delighted to announce that the latest update of Ensembl Genomes has been released. Highlights ? Updated names and descriptions for Strigamia maritima genes ? 777 new bacterial genomes (Ensembl Bacteria now contains 21,767genomes) ? Assemblies 2.40 and 2.50 of tomato available in Assembly Converter (to transfer genomic coordinates between assemblies) ? New variation data for the plant pathogens Verticillium dahliae (JR2 strain) and Zymoseptoria tritici Genome comparisons for Triticeae and related species Whole genome alignments between seven pairs of Triticeae genomes, including the bread wheat A, B and D component genomes, Triticum urartu (the A genome progenitor), Aegilops tauschii (the D genome progenitor), and barley are now available. The alignments were obtained using ATAC and the statistics on genome and coding exon coverages can be found on our website. MAF files on our FTP sites In response to several requests from our users we now provide the pairwise alignments as MAF files. These can be found on the FTP download site of all Ensembl Genomes divisions. Other news ? Fungi and Protists: Updated PHIbase annotation and protein domain information based on InterProScan ? Latest assemblies and gene sets for Medicago truncatula and Oryza meridionalis ? New RNASeq data in barley, Oryza sp and Leersia perrieri A complete list of both new and updated date can be found on our website. Any questions or comments? Email us at helpdesk at ensemblgenomes.org The Ensembl Genomes team -------------- next part -------------- An HTML attachment was scrubbed... URL: From dstaines at ebi.ac.uk Wed Mar 25 13:35:17 2015 From: dstaines at ebi.ac.uk (Dan Staines) Date: Wed, 25 Mar 2015 13:35:17 +0000 Subject: [ensembl-announce] Ensembl Genomes public MySQL data retention Message-ID: <5512B995.9010402@ebi.ac.uk> As the amount of data in each release of Ensembl Genomes increases, it has become necessary to restrict the number of past releases available on our public MySQL server (mysql-eg-publicsql.ebi.ac.uk). Towards the end of May 2015, shortly before the release 27 of Ensembl Genomes, all databases from all releases prior to release 18 will be removed. With each subsequent release, data from the oldest release will be removed at release time, leaving data from the most recent 10 releases only. The removal of each release will be announced with the intentions for the new release approximately 2 months in advance. Please note that the data available from our FTP site will be unaffected by this change in policy, with data from all releases of Ensembl Genomes remaining available in all supported formats, including full MySQL dumps. Regards, Dan Staines, on behalf of the Ensembl Genomes team. -- Dan Staines, PhD Ensembl Genomes Technical Coordinator EMBL-EBI Tel: +44-(0)1223-492507 Wellcome Trust Genome Campus Fax: +44-(0)1223-494468 Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/ From maurel at ebi.ac.uk Tue Mar 31 15:27:08 2015 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Tue, 31 Mar 2015 15:27:08 +0100 Subject: [ensembl-announce] GRCh37 release 79 data update Message-ID: <0F253C22-7B05-45F1-AA8E-AA1996B57145@ebi.ac.uk> Dear all, We are pleased to announce that the first Ensembl data update for human GRCh37 (e!79) has been released: http://grch37.ensembl.org/index.html Highlights include: Added variation data for human from dbSNP 142 Imported Genotypes from 1000 Genomes Phase 3 New regulatory build for human Imported latest release of public HGMD data (version 2014.4) Imported COSMIC data version 71 Added RefSeq GFF3 annotation A complete list of the changes can be found on: http://grch37.ensembl.org/info/website/news.html Also, for the latest news from the Ensembl project visit our blog at http://www.ensembl.info The GRCh37 release 79 blog post can be viewed here: http://www.ensembl.info/blog/2015/03/31/first-update-of-the-ensembl-grch37-site/ Regards, Thomas -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... 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