From maurel at ebi.ac.uk Thu Feb 7 13:39:20 2013 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Thu, 7 Feb 2013 13:39:20 +0000 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 71 Message-ID: <130C38A0-A912-424F-851F-B8F5FE8A4190@ebi.ac.uk> Dear all, Please find the summary of the declarations of intentions for Ensembl release 71 (scheduled for the 3rd of April 2013) 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 denise at ebi.ac.uk Fri Feb 8 09:13:22 2013 From: denise at ebi.ac.uk (denise at ebi.ac.uk) Date: Fri, 8 Feb 2013 09:13:22 -0000 Subject: [ensembl-announce] Ensembl Genomes release announcement Message-ID: <1825ae9c67309b3efbe6079830d57005.squirrel@webmail.ebi.ac.uk> Dear all, The Ensembl Genomes project is pleased to announce release 17 of Ensembl Genomes. Our latest release brings over 6,000 bacterial genomes into Ensembl for the first time ever! Users can browse these data interactively on the web with our graphical interface. Programmatic access is available through the Perl and RESTful Ensembl APIs, and through publicly accessible mysql databases. Full data dumps such as DNA sequence and protein sequence in FASTA format, annotations in GTF format, and mysql dump files are also provided on our FTP sites. Due to this sheer number of new genomes in Ensembl Bacteria in release 17, BioMart access is no longer possible and we are now working on alternative and more powerful data retrieval tools. An increased number of bacteria (over 120 genomes) has now been used for comparative genomics analyses across a wider range of non-bacterial genomes (from both Ensembl and Ensembl Genomes projects). This is known as Pan-taxonomic Compara and can be visualised in the gene views on the browser or accessed through the Compara database. In addition to the thousands of new bacterial genomes, we also have six new genomes in Ensembl Fungi and one new genome in Ensembl Protists. We have also improved existing genomes and added new variation, comparative genomics and transcriptomics data for several species. The significant milestones of this release are: Ensembl Bacteria: * Protein families are now classified based on PANTHER and HAMAP matches. Gene trees are provided for several but not for all bacterial genomes * Pan?taxonomic compara now contains 123 key bacterial genomes * Gene families are now populated by dividing all proteins on all genomes by HAMAP and PANTHER classification provided by InterPro Ensembl Fungi: * Six new genomes: Komagataella pastoris, Sporisorium reilianum, Pyrenophora teres, Pyrenophora tritici-repentis, Glomerella graminicola and Melampsora larici-populina * New EST alignments for Melampsora larici-populina, Glomerella graminicola and Leptosphaeria maculans * Mycosphaerella graminicola has been renamed to Zymoseptoria tritici Ensembl Metazoa: * Updated gene sets for Anopheles gambiae * Updated gene sets for Drosophila pseudoobscura (FlyBase version 2.30) and Drosophila simulans (FlyBase version 1.4) * Updated cross-references for all 12 drosophilid species * A missing chromosome in beetle (Tribolium castaneum) was also reinstated, and its gene models updated Ensembl Plants: * New and extensive variation dataset for Hordeum vulgare (barley) * Triticum aestivum (wheat) EST and RNA-seq alignments in the syntenic context of Brachypodium are now available * New wheat sequence search facility based on extensive genomic and transcriptomic data aligned to Brachypodium * Solanum tuberosum (potato) EST and RNA-seq alignments are also now available * New pairwise alignments between several plant genomes. Ensembl Protists: * A new genome of a flagellated protozoan parasite, Giardia lamblia, is now available Software migration to Ensembl 70 Have fun! The Ensembl Genomes Team From dstaines at ebi.ac.uk Mon Feb 18 16:58:51 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Mon, 18 Feb 2013 16:58:51 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 18 Message-ID: <51225DCB.1040602@ebi.ac.uk> Dear all, We would like to announce our intention to release version 18 of Ensembl Genomes on 16th April 2013. Our intended changes for this release are detailed here: http://ensemblgenomes.org/info/release18 Please note these are intentions and are therefore not guaranteed to be completed for April. Best 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 Thu Feb 7 13:39:20 2013 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Thu, 7 Feb 2013 13:39:20 +0000 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 71 Message-ID: <130C38A0-A912-424F-851F-B8F5FE8A4190@ebi.ac.uk> Dear all, Please find the summary of the declarations of intentions for Ensembl release 71 (scheduled for the 3rd of April 2013) 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 denise at ebi.ac.uk Fri Feb 8 09:13:22 2013 From: denise at ebi.ac.uk (denise at ebi.ac.uk) Date: Fri, 8 Feb 2013 09:13:22 -0000 Subject: [ensembl-announce] Ensembl Genomes release announcement Message-ID: <1825ae9c67309b3efbe6079830d57005.squirrel@webmail.ebi.ac.uk> Dear all, The Ensembl Genomes project is pleased to announce release 17 of Ensembl Genomes. Our latest release brings over 6,000 bacterial genomes into Ensembl for the first time ever! Users can browse these data interactively on the web with our graphical interface. Programmatic access is available through the Perl and RESTful Ensembl APIs, and through publicly accessible mysql databases. Full data dumps such as DNA sequence and protein sequence in FASTA format, annotations in GTF format, and mysql dump files are also provided on our FTP sites. Due to this sheer number of new genomes in Ensembl Bacteria in release 17, BioMart access is no longer possible and we are now working on alternative and more powerful data retrieval tools. An increased number of bacteria (over 120 genomes) has now been used for comparative genomics analyses across a wider range of non-bacterial genomes (from both Ensembl and Ensembl Genomes projects). This is known as Pan-taxonomic Compara and can be visualised in the gene views on the browser or accessed through the Compara database. In addition to the thousands of new bacterial genomes, we also have six new genomes in Ensembl Fungi and one new genome in Ensembl Protists. We have also improved existing genomes and added new variation, comparative genomics and transcriptomics data for several species. The significant milestones of this release are: Ensembl Bacteria: * Protein families are now classified based on PANTHER and HAMAP matches. Gene trees are provided for several but not for all bacterial genomes * Pan?taxonomic compara now contains 123 key bacterial genomes * Gene families are now populated by dividing all proteins on all genomes by HAMAP and PANTHER classification provided by InterPro Ensembl Fungi: * Six new genomes: Komagataella pastoris, Sporisorium reilianum, Pyrenophora teres, Pyrenophora tritici-repentis, Glomerella graminicola and Melampsora larici-populina * New EST alignments for Melampsora larici-populina, Glomerella graminicola and Leptosphaeria maculans * Mycosphaerella graminicola has been renamed to Zymoseptoria tritici Ensembl Metazoa: * Updated gene sets for Anopheles gambiae * Updated gene sets for Drosophila pseudoobscura (FlyBase version 2.30) and Drosophila simulans (FlyBase version 1.4) * Updated cross-references for all 12 drosophilid species * A missing chromosome in beetle (Tribolium castaneum) was also reinstated, and its gene models updated Ensembl Plants: * New and extensive variation dataset for Hordeum vulgare (barley) * Triticum aestivum (wheat) EST and RNA-seq alignments in the syntenic context of Brachypodium are now available * New wheat sequence search facility based on extensive genomic and transcriptomic data aligned to Brachypodium * Solanum tuberosum (potato) EST and RNA-seq alignments are also now available * New pairwise alignments between several plant genomes. Ensembl Protists: * A new genome of a flagellated protozoan parasite, Giardia lamblia, is now available Software migration to Ensembl 70 Have fun! The Ensembl Genomes Team From dstaines at ebi.ac.uk Mon Feb 18 16:58:51 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Mon, 18 Feb 2013 16:58:51 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 18 Message-ID: <51225DCB.1040602@ebi.ac.uk> Dear all, We would like to announce our intention to release version 18 of Ensembl Genomes on 16th April 2013. Our intended changes for this release are detailed here: http://ensemblgenomes.org/info/release18 Please note these are intentions and are therefore not guaranteed to be completed for April. Best 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/