From maurel at ebi.ac.uk Wed Aug 1 15:23:30 2012 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Wed, 1 Aug 2012 15:23:30 +0100 Subject: [ensembl-announce] Ensembl release 68 is out! Message-ID: The latest Ensembl update (e!68) has been released : http://www.ensembl.org/ Here are some highlights: Human: The patches for the human genome assembly have been updated to GRCh37.p8, Human somatic variants from COSMIC have been updated to release 59. Human structural variation has been updated and new studies have been added. New genomes: The assembly for Mouse has been updated to GRCm38 and Dog has been updated to CanFam3.1. New species: Chinese softshell turtle (Pelodiscus sinensis). Other news: We have moved to using Sequence Ontology terms to describe consequences in Ensembl Variation and starting with this release we will be incrementally refreshing the design of the Ensembl web template. A complete list of the changes in release 68 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/2012/07/12/ensembl-68-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 denise at ebi.ac.uk Tue Aug 7 14:56:01 2012 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Tue, 7 Aug 2012 14:56:01 +0100 Subject: [ensembl-announce] Ensembl Genomes 15 has been released! Message-ID: <2C6912FC-31DE-47AF-A285-4BCFE1CE4BF0@ebi.ac.uk> Dear all, The Ensembl Genomes Project is pleased to announce release 15 of Ensembl Genomes. This release contains two new genomes, bringing the total genomes supported to 354. Main highlights are: * Two new species in Ensembl Fungi: Leptosphaeria maculans and Trichoderma virens. New variation dataset is available for Puccinia graminis. * Cross-references to other databases have been updated for Ensembl Metazoa. * A set of homoeologous SNPs between wheat A, B and D genomes using wheat contigs aligned to Brachypodium distachyon as a reference framework is now available, a structural variation dataset for Sorghum bicolor has been imported from dGVA, and a variety of small improvements to our assembly, annotation and variation datasets have been incorporated. See the Ensembl Plants homepage for details. * RNA-Seq data from the ENA Sequence Read Archive have been aligned to the genomes of Pythium ultimum, Phytophthora sojae and Albugo laibachii. A variation database for Phytophthora infestans using ENA Sequence Read Archive of three different strains is now available. * Software migration to Ensembl 68 * New Frequently Asked Questions (FAQs) are now available for all domains of Ensembl Genomes. Have a question? Check if it's been asked before! If there is a FAQ missing you would like to see, contact us. The Ensembl Genomes Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From maurel at ebi.ac.uk Tue Aug 14 10:03:52 2012 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Tue, 14 Aug 2012 10:03:52 +0100 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 69 Message-ID: Dear all, Please find the summary of the declarations of intentions for Ensembl release 69 (scheduled for the 9th of October 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 Tue Aug 28 13:23:03 2012 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 28 Aug 2012 13:23:03 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 16 Intentions Message-ID: <503CB827.3080406@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 16 of Ensembl Genomes, due out on 23rd October 2012. Please note these are intentions and are therefore not guaranteed to be completed for October. These can also be viewed online at: http://ensemblgenomes.org/info/release16 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. Ensembl Genomes Release 16 Intentions General - Release scheduled for 23rd October 2012 - Update to Ensembl 69 software - Update of pan homology comparative genomics database to include latest versions of genomes from Ensembl and Ensembl Genomes Bacteria - No significant update planned Fungi - New data Addition of Fusarium oxysporum variation database based on sequencing of 23 different strains from the SRA - Updated data -- Puccinia graminis --- Import descriptions and gene names from Broad (where available) --- Add missing InterPro annotations --- Update ncRNA stable identifiers -- Add repeat features to Botryotinia fuckeliana -- Update Aspergillus contig names to use INSDC identifiers -- Updated BioMarts Protists - Updated data -- Add repeat features to Albugo laibachii -- Protein features for Hyaloperonospora arabidopsidis, Plasmodium falciparum and Tetrahymena thermophila -- Minor bugfixes for comparative genomics database -- Updated BioMarts Metazoa - New genomes -- Nasonia vitripennis (parasitic wasp) -- Anopheles darlingi (American malaria mosquito) - Updated genomes -- update Drosophila melanogaster to FlyBase 5.46 --- updated gene models --- updated variation consequences --- updated array mapping -- correction to Anopheles gambiae variation database to permit use of LD and transcript displays -- updated Caenorhabditis japonica gene models and assembly -- updated Caenorhabditis brenneri gene models and assembly -- updated Caenorhabditis remanei gene models and assembly -- updated Pristionchus pacificus cross-references - New data -- Variation dataset for Anopheles gambiae from insecticide resistance study from Liverpool School of Tropical Medicine - Updated data -- Updated comparative genomics --- Peptide --- Drosophilids DNA --- Worm DNA --- Mosquito DNA -- Updated BioMarts Plants - New genomes -- Hordeum vulgare (barley) -- Solanum tuberosum (potato) - Updated genomes -- Updated gene models for Glycine max (soybean) - New data -- Updated and improved Triticum aestivum (wheat) homoeologous SNPs and 'gene space' assembly alignments to Brachypodium distachyon (purple false brome) -- New EST alignments for Physcomitrella patens (moss) -- New repeats feature annotation for Selaginella moellendorffii (lycopod) -- New variation dataset for Sorghum bicolor (sorghum) - Updated data -- Update to peptide and DNA comparative genomics -- Clean up of non-translating genes in Vitis vinifera (grape) -- 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 maurel at ebi.ac.uk Wed Aug 1 15:23:30 2012 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Wed, 1 Aug 2012 15:23:30 +0100 Subject: [ensembl-announce] Ensembl release 68 is out! Message-ID: The latest Ensembl update (e!68) has been released : http://www.ensembl.org/ Here are some highlights: Human: The patches for the human genome assembly have been updated to GRCh37.p8, Human somatic variants from COSMIC have been updated to release 59. Human structural variation has been updated and new studies have been added. New genomes: The assembly for Mouse has been updated to GRCm38 and Dog has been updated to CanFam3.1. New species: Chinese softshell turtle (Pelodiscus sinensis). Other news: We have moved to using Sequence Ontology terms to describe consequences in Ensembl Variation and starting with this release we will be incrementally refreshing the design of the Ensembl web template. A complete list of the changes in release 68 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/2012/07/12/ensembl-68-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 denise at ebi.ac.uk Tue Aug 7 14:56:01 2012 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Tue, 7 Aug 2012 14:56:01 +0100 Subject: [ensembl-announce] Ensembl Genomes 15 has been released! Message-ID: <2C6912FC-31DE-47AF-A285-4BCFE1CE4BF0@ebi.ac.uk> Dear all, The Ensembl Genomes Project is pleased to announce release 15 of Ensembl Genomes. This release contains two new genomes, bringing the total genomes supported to 354. Main highlights are: * Two new species in Ensembl Fungi: Leptosphaeria maculans and Trichoderma virens. New variation dataset is available for Puccinia graminis. * Cross-references to other databases have been updated for Ensembl Metazoa. * A set of homoeologous SNPs between wheat A, B and D genomes using wheat contigs aligned to Brachypodium distachyon as a reference framework is now available, a structural variation dataset for Sorghum bicolor has been imported from dGVA, and a variety of small improvements to our assembly, annotation and variation datasets have been incorporated. See the Ensembl Plants homepage for details. * RNA-Seq data from the ENA Sequence Read Archive have been aligned to the genomes of Pythium ultimum, Phytophthora sojae and Albugo laibachii. A variation database for Phytophthora infestans using ENA Sequence Read Archive of three different strains is now available. * Software migration to Ensembl 68 * New Frequently Asked Questions (FAQs) are now available for all domains of Ensembl Genomes. Have a question? Check if it's been asked before! If there is a FAQ missing you would like to see, contact us. The Ensembl Genomes Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From maurel at ebi.ac.uk Tue Aug 14 10:03:52 2012 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Tue, 14 Aug 2012 10:03:52 +0100 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 69 Message-ID: Dear all, Please find the summary of the declarations of intentions for Ensembl release 69 (scheduled for the 9th of October 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 Tue Aug 28 13:23:03 2012 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 28 Aug 2012 13:23:03 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 16 Intentions Message-ID: <503CB827.3080406@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 16 of Ensembl Genomes, due out on 23rd October 2012. Please note these are intentions and are therefore not guaranteed to be completed for October. These can also be viewed online at: http://ensemblgenomes.org/info/release16 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. Ensembl Genomes Release 16 Intentions General - Release scheduled for 23rd October 2012 - Update to Ensembl 69 software - Update of pan homology comparative genomics database to include latest versions of genomes from Ensembl and Ensembl Genomes Bacteria - No significant update planned Fungi - New data Addition of Fusarium oxysporum variation database based on sequencing of 23 different strains from the SRA - Updated data -- Puccinia graminis --- Import descriptions and gene names from Broad (where available) --- Add missing InterPro annotations --- Update ncRNA stable identifiers -- Add repeat features to Botryotinia fuckeliana -- Update Aspergillus contig names to use INSDC identifiers -- Updated BioMarts Protists - Updated data -- Add repeat features to Albugo laibachii -- Protein features for Hyaloperonospora arabidopsidis, Plasmodium falciparum and Tetrahymena thermophila -- Minor bugfixes for comparative genomics database -- Updated BioMarts Metazoa - New genomes -- Nasonia vitripennis (parasitic wasp) -- Anopheles darlingi (American malaria mosquito) - Updated genomes -- update Drosophila melanogaster to FlyBase 5.46 --- updated gene models --- updated variation consequences --- updated array mapping -- correction to Anopheles gambiae variation database to permit use of LD and transcript displays -- updated Caenorhabditis japonica gene models and assembly -- updated Caenorhabditis brenneri gene models and assembly -- updated Caenorhabditis remanei gene models and assembly -- updated Pristionchus pacificus cross-references - New data -- Variation dataset for Anopheles gambiae from insecticide resistance study from Liverpool School of Tropical Medicine - Updated data -- Updated comparative genomics --- Peptide --- Drosophilids DNA --- Worm DNA --- Mosquito DNA -- Updated BioMarts Plants - New genomes -- Hordeum vulgare (barley) -- Solanum tuberosum (potato) - Updated genomes -- Updated gene models for Glycine max (soybean) - New data -- Updated and improved Triticum aestivum (wheat) homoeologous SNPs and 'gene space' assembly alignments to Brachypodium distachyon (purple false brome) -- New EST alignments for Physcomitrella patens (moss) -- New repeats feature annotation for Selaginella moellendorffii (lycopod) -- New variation dataset for Sorghum bicolor (sorghum) - Updated data -- Update to peptide and DNA comparative genomics -- Clean up of non-translating genes in Vitis vinifera (grape) -- 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/