From lg4 at ebi.ac.uk Mon Dec 12 16:34:35 2011 From: lg4 at ebi.ac.uk (Leo Gordon) Date: Mon, 12 Dec 2011 16:34:35 +0000 Subject: [ensembl-announce] Ensembl release 65 is out! Message-ID: We are happy to announce release 65 of Ensembl (http://www.ensembl.org) which was released on December 7th. Highlights include a new species; the Atlantic cod (Gadus morhua) assembly was provided by the Cod genome consortium, the most recent human and zebrafish manual gene annotations from HAVANA and a fresh update of mouse variation data, among numerous other additions. We have a new species; the Atlantic cod assembly provided by the Cod genome consortium, new version 2.1.4 of the Chimpanzee genome assembly, new high-coverage assembly OtoGar3 for bushbaby provided by the Broad Institute. The Ensembl Variation set for Human has been updated to dbSNP 134 and now includes over 40 million variants. For more information about this release visit: 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/2011/12/08/ensembl-65-has-been-released/ Best regards, Leo Gordon. From dstaines at ebi.ac.uk Fri Dec 16 15:00:27 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Fri, 16 Dec 2011 15:00:27 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 13 intentions Message-ID: <4EEB5D0B.9040205@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 13 of Ensembl Genomes, due out on 6th March 2012. Please note these are intentions and are therefore not guaranteed to be completed for March. These can also be viewed online at: http://ensemblgenomes.org/info/release13 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. General - release scheduled for 6th March 2012 - update to Ensembl 66 software - new Pan Compara database - updated pan concern databases Metazoa - addition of Trichinella spiralis genome - updated DNA compara database - updated peptide compara database - updated biomarts Bacteria - no significant updates planned Protists - addition of Toxoplasma gondii ME49 genome - updated peptide compara database - updated biomarts Fungi - addition of Magnaporthe oryzae genome - addition of Magnaporthe poae genome - addition of Gaeumannomyces graminis genome - Schizosaccharomyces pombe gene build update - updated peptide compara database - updated biomarts Plants - addition of Brassica rapa genome - oligo probe mappings for Zea mays - updated peptide compara database - 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 gspudich at ebi.ac.uk Fri Dec 16 14:48:02 2011 From: gspudich at ebi.ac.uk (Giulietta) Date: Fri, 16 Dec 2011 14:48:02 +0000 Subject: [ensembl-announce] Ensembl Genomes release 12 Message-ID: <4EEB5A22.4000405@ebi.ac.uk> The Ensembl Genomes Project is pleased to announce release 12 of Ensembl Genomes. This release contains 5 new genomes, bringing the total genomes supported to 335 . Main highlights are: * Software migration to Ensembl 65 * Operon data from RegulonDB for /E. coli K12/ in Ensembl Bacteria * A new species (/Ashbya gossypii ) /and manually curated annotation from a new resource for yeast! This is the first release of Ensembl Fungi containing data from PomBase , a new genome-centric resource (developed by Ensembl Genomes, the University of Cambridge, and University College London) for the fission yeast /Schizosaccharomyces pombe/ . *The addition of /Cyanidioschyzon merolae/ to Ensembl Plants and significant updates to /Physcomitrella patens/ and the soybean /Glycine max/ * Three new genomes in Ensembl Metazoa : /Atta cephalotes/ , a leaf-cutting ant, /Tribolium castaneum/ , the red flour beetle, and /Bombyx mori/ , a domesticated silkmoth /Note, EG 12 will be available on ftp next week./ Happy holidays! The Ensembl Genomes Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From dstaines at ebi.ac.uk Sat Dec 24 13:14:32 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Sat, 24 Dec 2011 13:14:32 +0000 Subject: [ensembl-announce] [Eg_internal] Ensembl Genomes release 12 In-Reply-To: <4EEB5A22.4000405@ebi.ac.uk> References: <4EEB5A22.4000405@ebi.ac.uk> Message-ID: <4EF5D038.90007@ebi.ac.uk> On 12/16/2011 02:48 PM, Giulietta wrote: > > /Note, EG 12 will be available on ftp next week./ We are happy to announce the availability of FTP data for EG12, and apologise for the late running of this service. Seasons greetings, Dan. -- 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 lg4 at ebi.ac.uk Mon Dec 12 16:34:35 2011 From: lg4 at ebi.ac.uk (Leo Gordon) Date: Mon, 12 Dec 2011 16:34:35 +0000 Subject: [ensembl-announce] Ensembl release 65 is out! Message-ID: We are happy to announce release 65 of Ensembl (http://www.ensembl.org) which was released on December 7th. Highlights include a new species; the Atlantic cod (Gadus morhua) assembly was provided by the Cod genome consortium, the most recent human and zebrafish manual gene annotations from HAVANA and a fresh update of mouse variation data, among numerous other additions. We have a new species; the Atlantic cod assembly provided by the Cod genome consortium, new version 2.1.4 of the Chimpanzee genome assembly, new high-coverage assembly OtoGar3 for bushbaby provided by the Broad Institute. The Ensembl Variation set for Human has been updated to dbSNP 134 and now includes over 40 million variants. For more information about this release visit: 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/2011/12/08/ensembl-65-has-been-released/ Best regards, Leo Gordon. From dstaines at ebi.ac.uk Fri Dec 16 15:00:27 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Fri, 16 Dec 2011 15:00:27 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 13 intentions Message-ID: <4EEB5D0B.9040205@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 13 of Ensembl Genomes, due out on 6th March 2012. Please note these are intentions and are therefore not guaranteed to be completed for March. These can also be viewed online at: http://ensemblgenomes.org/info/release13 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. General - release scheduled for 6th March 2012 - update to Ensembl 66 software - new Pan Compara database - updated pan concern databases Metazoa - addition of Trichinella spiralis genome - updated DNA compara database - updated peptide compara database - updated biomarts Bacteria - no significant updates planned Protists - addition of Toxoplasma gondii ME49 genome - updated peptide compara database - updated biomarts Fungi - addition of Magnaporthe oryzae genome - addition of Magnaporthe poae genome - addition of Gaeumannomyces graminis genome - Schizosaccharomyces pombe gene build update - updated peptide compara database - updated biomarts Plants - addition of Brassica rapa genome - oligo probe mappings for Zea mays - updated peptide compara database - 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 gspudich at ebi.ac.uk Fri Dec 16 14:48:02 2011 From: gspudich at ebi.ac.uk (Giulietta) Date: Fri, 16 Dec 2011 14:48:02 +0000 Subject: [ensembl-announce] Ensembl Genomes release 12 Message-ID: <4EEB5A22.4000405@ebi.ac.uk> The Ensembl Genomes Project is pleased to announce release 12 of Ensembl Genomes. This release contains 5 new genomes, bringing the total genomes supported to 335 . Main highlights are: * Software migration to Ensembl 65 * Operon data from RegulonDB for /E. coli K12/ in Ensembl Bacteria * A new species (/Ashbya gossypii ) /and manually curated annotation from a new resource for yeast! This is the first release of Ensembl Fungi containing data from PomBase , a new genome-centric resource (developed by Ensembl Genomes, the University of Cambridge, and University College London) for the fission yeast /Schizosaccharomyces pombe/ . *The addition of /Cyanidioschyzon merolae/ to Ensembl Plants and significant updates to /Physcomitrella patens/ and the soybean /Glycine max/ * Three new genomes in Ensembl Metazoa : /Atta cephalotes/ , a leaf-cutting ant, /Tribolium castaneum/ , the red flour beetle, and /Bombyx mori/ , a domesticated silkmoth /Note, EG 12 will be available on ftp next week./ Happy holidays! The Ensembl Genomes Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From dstaines at ebi.ac.uk Sat Dec 24 13:14:32 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Sat, 24 Dec 2011 13:14:32 +0000 Subject: [ensembl-announce] [Eg_internal] Ensembl Genomes release 12 In-Reply-To: <4EEB5A22.4000405@ebi.ac.uk> References: <4EEB5A22.4000405@ebi.ac.uk> Message-ID: <4EF5D038.90007@ebi.ac.uk> On 12/16/2011 02:48 PM, Giulietta wrote: > > /Note, EG 12 will be available on ftp next week./ We are happy to announce the availability of FTP data for EG12, and apologise for the late running of this service. Seasons greetings, Dan. -- 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/