From hr5 at sanger.ac.uk Fri Mar 2 09:28:04 2012 From: hr5 at sanger.ac.uk (Harpreet Riat) Date: Fri, 2 Mar 2012 09:28:04 +0000 Subject: [ensembl-announce] Ensembl release 66 is out! In-Reply-To: <979AA392-5246-454E-BE39-E31ECC0D74AB@sanger.ac.uk> References: <979AA392-5246-454E-BE39-E31ECC0D74AB@sanger.ac.uk> Message-ID: <975BC82A-110C-4594-ADD2-826EBE581703@sanger.ac.uk> We are happy to announce the launch of our latest Ensembl release (e66): http://www.ensembl.org/ Here are some highlights: Human: The human genome assembly is updated to GRCh37.p6, containing 124 assembly patches. The DNA sequence for the primary assembly (chromosomes 1-22, X, Y, unlocalized scaffolds and unplaced scaffolds) remains unchanged. The short sequence variants are now updated to dbSNP 135. A new regulatory consequence table shows regulatory features and motifs at the position of the SNP or other sequence variant. New species: Coelacanth (Latimeria chalumnae) New genome: The assembly for Ciona intestinalis is updated. A complete list of the changes in release 66 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/ Best regards, Harpreet -------------- next part -------------- An HTML attachment was scrubbed... URL: From denise at ebi.ac.uk Wed Mar 7 09:15:30 2012 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Wed, 7 Mar 2012 09:15:30 +0000 Subject: [ensembl-announce] Ensembl Genomes release announcement Message-ID: <72A2D9B4-F2A1-4F15-828A-AAC0C5908F6D@ebi.ac.uk> Dear all, The Ensembl Genomes Project is pleased to announce release 13 of Ensembl Genomes. This release contains 6 new genomes, bringing the total genomes supported to 341. Main highlights are: * Software migration to Ensembl 66 * The addition of Brassica rapa to Ensembl Plants, as well as synteny data for species in the Arabidopsis and Oryza genomes and new oligo probe mapping from the GeneChip Maize Genome Array for Zea mays * A new species (Toxoplasma gondii ME49) added to Ensembl Protists and the genome of Trichinella spiralis is now available in Ensembl Metazoa. * Three new genomes in Ensembl Fungi: Magnaporthe oryzae, Magnaporthe poae and Gaeumannomyces graminis. There is also synteny data for species in the Saccharomycetales and Hypocrealestaxonomy groups. The annotation for S. pombe has been updated to reflect the most recent content from PomBase. * EMBL-EBI and Rothamsted Research have recently announced the release of the PhytoPath portal, a joint project bringing together Ensembl Genomes with PHI-base, a community-curated resource describing the role of genes in pathogenic infection. Genomes of pathogenic organisms from this project including the causative agents of diseases such as potato blight, rice blast and wheat rust can be found in this release of Ensembl Genomes. The Ensembl Genomes Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From maurel at ebi.ac.uk Wed Mar 7 11:49:46 2012 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Wed, 7 Mar 2012 11:49:46 +0000 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 67 Message-ID: <8A106898-6892-436D-AD2D-DB4124B48201@ebi.ac.uk> Please find the summary of the declarations of intentions for release 67 (scheduled for the 8th of May 2012) on our public website : admin.ensembl.org/Changelog/Summary. Note these are intentions and are not guaranteed to be in the release. 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 dstaines at ebi.ac.uk Wed Mar 14 14:47:38 2012 From: dstaines at ebi.ac.uk (Dan Staines) Date: Wed, 14 Mar 2012 14:47:38 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 14 intentions Message-ID: <4F60AF8A.5060603@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 14 of Ensembl Genomes, due out on 22nd May 2012. Please note these are intentions and are therefore not guaranteed to be completed for May. These can also be viewed online at: http://ensemblgenomes.org/info/release14 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. Ensembl Genomes Release 14 Intentions General - release scheduled for 22nd May 2012 - update to Ensembl 67 software - new Pan Compara database (to include Solanum lycopersicum) - updated pan concern databases - Updated and standardised metadata -- updated use of meta keys for names (as for Ensembl 67) -- standardisation of gene.version usage -- annotation of assemblies with Genome Collections identifiers Metazoa - New core database for Heliconius melpomene - New core database for Danaus plexippus - Updated core database with new assembly for Caenorhabditis briggsae - Updated core database with new gene set for Caenorhabditis elegans - Updated core database with new gene set for Aedes aegypti - Updated core database with new gene set for Culex quinquefasciatus - Updated core database with new gene set for Ixodes scapularis - Updated variation database for Drosophila melanogaster - Updated DNA compara containing pair-wise alignments for nematode species - Updated peptide compara - Updated biomart Bacteria - update to peptide compara to address some interface problems Protists - New core database for Hyaloperonospora arabidopsis - New core database for Albugo laibachii - New core database for Entamoeba histolytica - Updated synteny compara for Plasmodia and diatoms - New DNA compara database containing pair wise alignments for Peronosporales and Trypanosomatidae - New DNA compara database containing synteny for Trypanosomatidae - Updated peptide compara database - Updated biomarts Fungi - New core database for Sclerotinia sclerotorium - New core database for Botrytis conerea - Updated core database for Schizosaccharomyces pombe - Updated EST alignments for Magnaporthe oryzae - Updated peptide compara database - Updated biomarts Plants - New core database for Solanum lycopersicum - New core database for Solanum tuberosum - New core database for Oryza brachyantha - Updated core database for Brassica rapa to include updated xrefs (including projected GO terms) and ncRNA gene predictions - New otherfeaturese database for Brassica rapa to include EST mapping - New otherfeaturese database for Brachypodium distachyon to include wheat genespace alignments - New variation database for Oryza brachyantha - New DNA compara database containing pair-wise alignments for Solanaceae - Updated DNA compara database containing pair-wise alignments for Oryzeae - Updated peptide compara - Updated biomarts -- 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 ap5 at sanger.ac.uk Thu Mar 29 11:04:45 2012 From: ap5 at sanger.ac.uk (Anne Parker) Date: Thu, 29 Mar 2012 11:04:45 +0100 Subject: [ensembl-announce] Archive retirement reminder Message-ID: As per our earlier announcement, we will be retiring Ensembl archives 50-52 tomorrow, 30th March. Data and code for these releases will still be available to download, but the associated website will no longer be online. Cheers Anne Anne Parker Ensembl Web Production Manager http://www.ensembl.org From hr5 at sanger.ac.uk Fri Mar 2 09:28:04 2012 From: hr5 at sanger.ac.uk (Harpreet Riat) Date: Fri, 2 Mar 2012 09:28:04 +0000 Subject: [ensembl-announce] Ensembl release 66 is out! In-Reply-To: <979AA392-5246-454E-BE39-E31ECC0D74AB@sanger.ac.uk> References: <979AA392-5246-454E-BE39-E31ECC0D74AB@sanger.ac.uk> Message-ID: <975BC82A-110C-4594-ADD2-826EBE581703@sanger.ac.uk> We are happy to announce the launch of our latest Ensembl release (e66): http://www.ensembl.org/ Here are some highlights: Human: The human genome assembly is updated to GRCh37.p6, containing 124 assembly patches. The DNA sequence for the primary assembly (chromosomes 1-22, X, Y, unlocalized scaffolds and unplaced scaffolds) remains unchanged. The short sequence variants are now updated to dbSNP 135. A new regulatory consequence table shows regulatory features and motifs at the position of the SNP or other sequence variant. New species: Coelacanth (Latimeria chalumnae) New genome: The assembly for Ciona intestinalis is updated. A complete list of the changes in release 66 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/ Best regards, Harpreet -------------- next part -------------- An HTML attachment was scrubbed... URL: From denise at ebi.ac.uk Wed Mar 7 09:15:30 2012 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Wed, 7 Mar 2012 09:15:30 +0000 Subject: [ensembl-announce] Ensembl Genomes release announcement Message-ID: <72A2D9B4-F2A1-4F15-828A-AAC0C5908F6D@ebi.ac.uk> Dear all, The Ensembl Genomes Project is pleased to announce release 13 of Ensembl Genomes. This release contains 6 new genomes, bringing the total genomes supported to 341. Main highlights are: * Software migration to Ensembl 66 * The addition of Brassica rapa to Ensembl Plants, as well as synteny data for species in the Arabidopsis and Oryza genomes and new oligo probe mapping from the GeneChip Maize Genome Array for Zea mays * A new species (Toxoplasma gondii ME49) added to Ensembl Protists and the genome of Trichinella spiralis is now available in Ensembl Metazoa. * Three new genomes in Ensembl Fungi: Magnaporthe oryzae, Magnaporthe poae and Gaeumannomyces graminis. There is also synteny data for species in the Saccharomycetales and Hypocrealestaxonomy groups. The annotation for S. pombe has been updated to reflect the most recent content from PomBase. * EMBL-EBI and Rothamsted Research have recently announced the release of the PhytoPath portal, a joint project bringing together Ensembl Genomes with PHI-base, a community-curated resource describing the role of genes in pathogenic infection. Genomes of pathogenic organisms from this project including the causative agents of diseases such as potato blight, rice blast and wheat rust can be found in this release of Ensembl Genomes. The Ensembl Genomes Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From maurel at ebi.ac.uk Wed Mar 7 11:49:46 2012 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Wed, 7 Mar 2012 11:49:46 +0000 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 67 Message-ID: <8A106898-6892-436D-AD2D-DB4124B48201@ebi.ac.uk> Please find the summary of the declarations of intentions for release 67 (scheduled for the 8th of May 2012) on our public website : admin.ensembl.org/Changelog/Summary. Note these are intentions and are not guaranteed to be in the release. 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 dstaines at ebi.ac.uk Wed Mar 14 14:47:38 2012 From: dstaines at ebi.ac.uk (Dan Staines) Date: Wed, 14 Mar 2012 14:47:38 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 14 intentions Message-ID: <4F60AF8A.5060603@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 14 of Ensembl Genomes, due out on 22nd May 2012. Please note these are intentions and are therefore not guaranteed to be completed for May. These can also be viewed online at: http://ensemblgenomes.org/info/release14 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. Ensembl Genomes Release 14 Intentions General - release scheduled for 22nd May 2012 - update to Ensembl 67 software - new Pan Compara database (to include Solanum lycopersicum) - updated pan concern databases - Updated and standardised metadata -- updated use of meta keys for names (as for Ensembl 67) -- standardisation of gene.version usage -- annotation of assemblies with Genome Collections identifiers Metazoa - New core database for Heliconius melpomene - New core database for Danaus plexippus - Updated core database with new assembly for Caenorhabditis briggsae - Updated core database with new gene set for Caenorhabditis elegans - Updated core database with new gene set for Aedes aegypti - Updated core database with new gene set for Culex quinquefasciatus - Updated core database with new gene set for Ixodes scapularis - Updated variation database for Drosophila melanogaster - Updated DNA compara containing pair-wise alignments for nematode species - Updated peptide compara - Updated biomart Bacteria - update to peptide compara to address some interface problems Protists - New core database for Hyaloperonospora arabidopsis - New core database for Albugo laibachii - New core database for Entamoeba histolytica - Updated synteny compara for Plasmodia and diatoms - New DNA compara database containing pair wise alignments for Peronosporales and Trypanosomatidae - New DNA compara database containing synteny for Trypanosomatidae - Updated peptide compara database - Updated biomarts Fungi - New core database for Sclerotinia sclerotorium - New core database for Botrytis conerea - Updated core database for Schizosaccharomyces pombe - Updated EST alignments for Magnaporthe oryzae - Updated peptide compara database - Updated biomarts Plants - New core database for Solanum lycopersicum - New core database for Solanum tuberosum - New core database for Oryza brachyantha - Updated core database for Brassica rapa to include updated xrefs (including projected GO terms) and ncRNA gene predictions - New otherfeaturese database for Brassica rapa to include EST mapping - New otherfeaturese database for Brachypodium distachyon to include wheat genespace alignments - New variation database for Oryza brachyantha - New DNA compara database containing pair-wise alignments for Solanaceae - Updated DNA compara database containing pair-wise alignments for Oryzeae - Updated peptide compara - Updated biomarts -- 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 ap5 at sanger.ac.uk Thu Mar 29 11:04:45 2012 From: ap5 at sanger.ac.uk (Anne Parker) Date: Thu, 29 Mar 2012 11:04:45 +0100 Subject: [ensembl-announce] Archive retirement reminder Message-ID: As per our earlier announcement, we will be retiring Ensembl archives 50-52 tomorrow, 30th March. Data and code for these releases will still be available to download, but the associated website will no longer be online. Cheers Anne Anne Parker Ensembl Web Production Manager http://www.ensembl.org