From amonida at ebi.ac.uk Thu Oct 8 13:21:10 2015 From: amonida at ebi.ac.uk (Amonida Zadissa) Date: Thu, 08 Oct 2015 13:21:10 +0100 Subject: [ensembl-announce] Ensembl GRCh37 second data update Message-ID: <56165FB6.3010401@ebi.ac.uk> Dear all, We are pleased to announce that the first Ensembl data update for human GRCh37 (e82) has been released: http://grch37.ensembl.org/index.html Highlights include: * dbSNP144 human data including data from the Exome Aggregation Consortium (ExAC) * Public HGMD data (version 2015.2) * Phenotype data from NHGRI-EBI GWAS, OMIM, ClinVar, UniProt, Orphanet and Decipher * Exome Sequencing Project data (v.0.0.30. (Nov. 3, 2014)) * HumanCoreExome-12 chip * Gene annotation dumps in GFF3 format 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 82 blog post can be viewed here: http://www.ensembl.info/blog/2015/10/07/second-update-of-the-ensembl-grch37-site/. Best regards, Amonida -- Amonida Zadissa Ensembl Production team EMBL-EBI Wellcome Trust Genome Campus Hinxton CB10 1SD England From amonida at ebi.ac.uk Thu Oct 8 13:36:08 2015 From: amonida at ebi.ac.uk (Amonida Zadissa) Date: Thu, 08 Oct 2015 13:36:08 +0100 Subject: [ensembl-announce] Ensembl GRCh37 second data update In-Reply-To: <56165FB6.3010401@ebi.ac.uk> References: <56165FB6.3010401@ebi.ac.uk> Message-ID: <56166338.2010400@ebi.ac.uk> Apologies for the incorrect URL for the post. The correct link is: http://www.ensembl.info/blog/2015/10/08/second-update-of-the-ensembl-grch37-site/ Thanks, Amonida On 08/10/2015 13:21, Amonida Zadissa wrote: > Dear all, > > We are pleased to announce that the first Ensembl data update for human > GRCh37 (e82) has been released: http://grch37.ensembl.org/index.html > > Highlights include: > > * dbSNP144 human data including data from the Exome Aggregation > Consortium (ExAC) > * Public HGMD data (version 2015.2) > * Phenotype data from NHGRI-EBI GWAS, OMIM, ClinVar, UniProt, Orphanet > and Decipher > * Exome Sequencing Project data (v.0.0.30. (Nov. 3, 2014)) > * HumanCoreExome-12 chip > * Gene annotation dumps in GFF3 format > > > 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 82 blog post can be viewed here: > http://www.ensembl.info/blog/2015/10/07/second-update-of-the-ensembl-grch37-site/. > > > Best regards, > Amonida > > -- > Amonida Zadissa > Ensembl Production team > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > CB10 1SD > England From denise at ebi.ac.uk Fri Oct 16 16:23:05 2015 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Fri, 16 Oct 2015 16:23:05 +0100 Subject: [ensembl-announce] Ensembl Genomes release 29 is out! Message-ID: <59F87DD2-FB70-4CDB-8DA8-226C3CF9DFD6@ebi.ac.uk> Dear all, We are delighted to announce that the latest update of Ensembl Genomes has been released. Highlights of this release include: ? Pairwise alignments for more than 50 plant genomes including potato and tomato, cacao and grape, and several Oryza sp ? Newly available genomes from INSDC into our ever expanding Protists and Fungi divisions ? Cross-references of genes in Fungi and Protists to the Pathogen ? Host Interaction Database (PHI-base) ? Additional 6,806 bacterial genomes imported from ENA ? Protein domain information from InterProScan (version 5.14-53.0) Genomic alignments New pairwise alignments have been extended to additional plant genomes and can be viewed in our browser website. The alignment text can be downloaded in different file formats. Whole genome alignments can also be retrieved via our FTP or programmatically using our APIs. View the complete list of genomic alignments available in this new release. Marking your favourite region, gene, exon, or variant You can now mark a selected region when browsing the Ensembl Genomes websites. Drag and select your favourite gene and use the pop-up window to mark it. You can also click on the gene itself to mark the location of it. Other news Updated BioMart: Protists, Metazoa, Fungi and Plants Updated peptide comparative genomics New assemblies and annotations for existing fungal species Gene families available in Protists A complete list of the changes can be found on the Ensembl Genomes website. Any questions or comments? Get in touch . Best wishes, Denise and the Ensembl Genomes team @ensemblgenomes -------------- next part -------------- An HTML attachment was scrubbed... URL: From maurel at ebi.ac.uk Mon Oct 19 13:05:30 2015 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Mon, 19 Oct 2015 13:05:30 +0100 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 83 Message-ID: <24C4E6A8-9761-4D68-80A4-9A9536B41C6A@ebi.ac.uk> Dear all, Please find the summary of the declarations of intentions for Ensembl release 83 (scheduled for the 7th of December 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 dstaines at ebi.ac.uk Tue Oct 20 12:14:25 2015 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 20 Oct 2015 12:14:25 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 30 Intentions Message-ID: <56262211.5060309@ebi.ac.uk> Release 30 of Ensembl Genomes is scheduled for 17th December 2015 - our intentions for this release can be found here: http://ensemblgenomes.org/info/release/30 Please note these are intentions and are therefore not guaranteed to be completed for October. Best regards, Dan Staines, on behalf of the Ensembl Genomes team. -- Dan Staines, PhD Genomics Technology Infrastructure Coordinator EMBL-EBI, Wellcome Trust Genome Campus Cambridge CB10 1SD, UK Tel: +44-(0)1223-492507 From amonida at ebi.ac.uk Thu Oct 8 13:21:10 2015 From: amonida at ebi.ac.uk (Amonida Zadissa) Date: Thu, 08 Oct 2015 13:21:10 +0100 Subject: [ensembl-announce] Ensembl GRCh37 second data update Message-ID: <56165FB6.3010401@ebi.ac.uk> Dear all, We are pleased to announce that the first Ensembl data update for human GRCh37 (e82) has been released: http://grch37.ensembl.org/index.html Highlights include: * dbSNP144 human data including data from the Exome Aggregation Consortium (ExAC) * Public HGMD data (version 2015.2) * Phenotype data from NHGRI-EBI GWAS, OMIM, ClinVar, UniProt, Orphanet and Decipher * Exome Sequencing Project data (v.0.0.30. (Nov. 3, 2014)) * HumanCoreExome-12 chip * Gene annotation dumps in GFF3 format 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 82 blog post can be viewed here: http://www.ensembl.info/blog/2015/10/07/second-update-of-the-ensembl-grch37-site/. Best regards, Amonida -- Amonida Zadissa Ensembl Production team EMBL-EBI Wellcome Trust Genome Campus Hinxton CB10 1SD England From amonida at ebi.ac.uk Thu Oct 8 13:36:08 2015 From: amonida at ebi.ac.uk (Amonida Zadissa) Date: Thu, 08 Oct 2015 13:36:08 +0100 Subject: [ensembl-announce] Ensembl GRCh37 second data update In-Reply-To: <56165FB6.3010401@ebi.ac.uk> References: <56165FB6.3010401@ebi.ac.uk> Message-ID: <56166338.2010400@ebi.ac.uk> Apologies for the incorrect URL for the post. The correct link is: http://www.ensembl.info/blog/2015/10/08/second-update-of-the-ensembl-grch37-site/ Thanks, Amonida On 08/10/2015 13:21, Amonida Zadissa wrote: > Dear all, > > We are pleased to announce that the first Ensembl data update for human > GRCh37 (e82) has been released: http://grch37.ensembl.org/index.html > > Highlights include: > > * dbSNP144 human data including data from the Exome Aggregation > Consortium (ExAC) > * Public HGMD data (version 2015.2) > * Phenotype data from NHGRI-EBI GWAS, OMIM, ClinVar, UniProt, Orphanet > and Decipher > * Exome Sequencing Project data (v.0.0.30. (Nov. 3, 2014)) > * HumanCoreExome-12 chip > * Gene annotation dumps in GFF3 format > > > 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 82 blog post can be viewed here: > http://www.ensembl.info/blog/2015/10/07/second-update-of-the-ensembl-grch37-site/. > > > Best regards, > Amonida > > -- > Amonida Zadissa > Ensembl Production team > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > CB10 1SD > England From denise at ebi.ac.uk Fri Oct 16 16:23:05 2015 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Fri, 16 Oct 2015 16:23:05 +0100 Subject: [ensembl-announce] Ensembl Genomes release 29 is out! Message-ID: <59F87DD2-FB70-4CDB-8DA8-226C3CF9DFD6@ebi.ac.uk> Dear all, We are delighted to announce that the latest update of Ensembl Genomes has been released. Highlights of this release include: ? Pairwise alignments for more than 50 plant genomes including potato and tomato, cacao and grape, and several Oryza sp ? Newly available genomes from INSDC into our ever expanding Protists and Fungi divisions ? Cross-references of genes in Fungi and Protists to the Pathogen ? Host Interaction Database (PHI-base) ? Additional 6,806 bacterial genomes imported from ENA ? Protein domain information from InterProScan (version 5.14-53.0) Genomic alignments New pairwise alignments have been extended to additional plant genomes and can be viewed in our browser website. The alignment text can be downloaded in different file formats. Whole genome alignments can also be retrieved via our FTP or programmatically using our APIs. View the complete list of genomic alignments available in this new release. Marking your favourite region, gene, exon, or variant You can now mark a selected region when browsing the Ensembl Genomes websites. Drag and select your favourite gene and use the pop-up window to mark it. You can also click on the gene itself to mark the location of it. Other news Updated BioMart: Protists, Metazoa, Fungi and Plants Updated peptide comparative genomics New assemblies and annotations for existing fungal species Gene families available in Protists A complete list of the changes can be found on the Ensembl Genomes website. Any questions or comments? Get in touch . Best wishes, Denise and the Ensembl Genomes team @ensemblgenomes -------------- next part -------------- An HTML attachment was scrubbed... URL: From maurel at ebi.ac.uk Mon Oct 19 13:05:30 2015 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Mon, 19 Oct 2015 13:05:30 +0100 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 83 Message-ID: <24C4E6A8-9761-4D68-80A4-9A9536B41C6A@ebi.ac.uk> Dear all, Please find the summary of the declarations of intentions for Ensembl release 83 (scheduled for the 7th of December 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 dstaines at ebi.ac.uk Tue Oct 20 12:14:25 2015 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 20 Oct 2015 12:14:25 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 30 Intentions Message-ID: <56262211.5060309@ebi.ac.uk> Release 30 of Ensembl Genomes is scheduled for 17th December 2015 - our intentions for this release can be found here: http://ensemblgenomes.org/info/release/30 Please note these are intentions and are therefore not guaranteed to be completed for October. Best regards, Dan Staines, on behalf of the Ensembl Genomes team. -- Dan Staines, PhD Genomics Technology Infrastructure Coordinator EMBL-EBI, Wellcome Trust Genome Campus Cambridge CB10 1SD, UK Tel: +44-(0)1223-492507