From denise at ebi.ac.uk Mon Apr 7 15:53:36 2014 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Mon, 7 Apr 2014 15:53:36 +0100 Subject: [ensembl-announce] Ensembl Genomes release 22 is out! Message-ID: <03E621CE-53FD-4913-8453-6EE11D6387CE@ebi.ac.uk> Dear all, We are delighted to announce that the latest update of Ensembl Genomes has been released. The highlights of release 22 are: New Genomes Ensembl Plants Amborella trichopoda Prunus persica (peach) Oryza (rice) genomes: O. barthii, O. glumaepatula, O. meridionalis, O. nivara, and O. punctate Ensembl Protists Bigelowiella natans Pythium (plant pathogens) genomes: P. aphanidermatum, P. arrhenomanes, P. irregulare, P. iwayamai, P. ultimum, and P. vexans Ensembl Metazoa Onchocerca volvulus Ensembl Bacteria 1,246 additional genomes (11,010 genomes now represented in total) New data Ensembl Plants Sorghum bicolor variation data based on the SAP panel (Morris et. al. 2013) Homoeologous genes between the wheat component A, B and D genomes Whole genome alignments Inter-homoleogue alignments between the wheat A, B and D genomes, and integration with the gene trees Between Amborella trichopoda and Arabidopsis thaliana, and Amborella trichopoda and Oriza sativa Japonica Between the five new rice genomes and O. sativa Japonica, as well as against each other new rice genome Updated data Ensembl Fungi Latest annotations for S. pombe from PomBase GO annotation projected from S cerevisiae and S pombe to all species Ensembl Metazoa Latest EST-based genes for many species Removal of haplotype regions in Anopheles gambiae Peptide comparative genomes Ensembl Plants Updated UniGene alignments in T. aestivum against its progenitors Peptide comparative genomes Questions or comments? Drop us a line at helpdesk at ensemblgenomes.org The Ensembl Genomes team -------------- next part -------------- An HTML attachment was scrubbed... URL: From rhoda at ebi.ac.uk Mon Apr 7 16:20:30 2014 From: rhoda at ebi.ac.uk (Rhoda Kinsella) Date: Mon, 7 Apr 2014 16:20:30 +0100 Subject: [ensembl-announce] Ensembl Pre! site with new Human GRCh38, Amazon molly, crab-eating macaque and hedgehog now available! Message-ID: Dear all, We are pleased to announce that the initial annotation of the new human assembly, GRCh38, is now live on Ensembl Pre! http://pre.ensembl.org/Homo_sapiens/Info/Index/ Highlights of GRCh38 Pre! include: Preliminary gene set including annotation on alternative loci (e.g. MHC haplotypes, LRC region) Centromeres covering 2% of the genome GENCODE 19 models mapped from e!75 (i.e. from GRCh37) CCDS models mapped from e!75 RefSeq annotation release 106 models Human-specific cDNA and EST alignments Computed consequences of variants overlapping an Ensembl transcript using the projected Ensembl gene set (Download GVF and VCF files from Pre! FTP site) Computed consequences for variants overlapping NCBI?s RefSeq transcripts (Download GVF and VCF files from Pre! FTP site) Pre! site has been updated to use Solr search In addition to human we're pleased to announce that we also have Pre! sites available for amazon molly, crab-eating macaque and hedgehog. Keep an eye out for further GRCh38 annotation updates by checking the blog category GRCh38. The Ensembl Pre! blog post with details about the GRCh38 annotation can be viewed here: http://www.ensembl.info/blog/2014/04/07/pre-site-for-the-new-human-assembly-grch38-is-live/ We'll be running a free 20 minute webinar about the data on Ensembl Pre! on Wed 16 April at 4PM BST. To register, click on the following link: https://attendee.gototraining.com/r/8084872084204567809 Regards, Rhoda Rhoda Kinsella Ph.D. Ensembl Production Project Leader European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD -------------- next part -------------- An HTML attachment was scrubbed... URL: From gspudich at ebi.ac.uk Tue Apr 15 11:06:11 2014 From: gspudich at ebi.ac.uk (Giulietta) Date: Tue, 15 Apr 2014 11:06:11 +0100 Subject: [ensembl-announce] Free Ensembl Webinar on Pre! - Human GRCh38, Amazon molly, crab-eating macaque and hedgehog In-Reply-To: <13CBDE6A-95BE-43D6-AE01-79BDCDF1B06A@ebi.ac.uk> References: <13CBDE6A-95BE-43D6-AE01-79BDCDF1B06A@ebi.ac.uk> Message-ID: <534D0493.7080408@ebi.ac.uk> Reminder: we offer a free 20 minute webinar tomorrow (Wednesday, 4PM BST) on what's available on Pre! Sign up here: https://attendee.gototraining.com/r/8084872084204567809 Best wishes, Ensembl Outreach On 07/04/2014 16:20, Rhoda Kinsella wrote: > Dear all, > We are pleased to announce that the initial annotation of the new > human assembly, GRCh38, is now live on Ensembl Pre! > http://pre.ensembl.org/Homo_sapiens/Info/Index/ > > > *Highlights of GRCh38 Pre! include:* > > * Preliminary gene set including annotation on alternative loci > (e.g. MHC haplotypes, LRC region) > * Centromeres covering 2% of the genome > * GENCODE 19 models mapped from e!75 (i.e. from GRCh37) > * CCDS models mapped from e!75 > * RefSeq annotation release 106 models > * Human-specific cDNA and EST alignments > * Computed consequences of variants overlapping an Ensembl > transcript using the projected Ensembl gene set (Download GVF and > VCF files from Pre! FTP site ) > * Computed consequences for variants overlapping NCBI's RefSeq > transcripts (Download GVF and VCF files from Pre! FTP site > ) > * Pre! site has been updated to use Solr search > > > In addition to human we're pleased to announce that we also have Pre! > sites available for a > mazon molly > , crab-eating > macaque and > hedgehog . > > Keep an eye out for further GRCh38 annotation updates by checking the > blog category GRCh38 > . > > The Ensembl Pre! blog post with details about the GRCh38 annotation > can be viewed here: > http://www.ensembl.info/blog/2014/04/07/pre-site-for-the-new-human-assembly-grch38-is-live/ > > We'll be running a free 20 minute webinar about the data on Ensembl > Pre! on Wed 16 April at 4PM BST. To register, click on the following > link: https://attendee.gototraining.com/r/8084872084204567809 > > Regards, > Rhoda > > > Rhoda Kinsella Ph.D. > Ensembl Production Project Leader > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Trust Genome Campus > Hinxton, > Cambridge > CB10 1SD > > > > > > > _______________________________________________ > Ensembl-campus mailing list > Ensembl-campus at ebi.ac.uk > http://listserver.ebi.ac.uk/mailman/listinfo/ensembl-campus -------------- next part -------------- An HTML attachment was scrubbed... URL: From amonida at ebi.ac.uk Wed Apr 23 10:17:47 2014 From: amonida at ebi.ac.uk (Amonida Zadissa) Date: Wed, 23 Apr 2014 10:17:47 +0100 Subject: [ensembl-announce] Declarations of intentions for Ensembl release 76 Message-ID: <5357853B.2030900@ebi.ac.uk> Dear all, Please find the summary of the declarations of intentions for Ensembl release 76 (scheduled for the 24th of July 2014) on our public website: http://admin.ensembl.org/Changelog/Summary Note these are intentions and are not guaranteed to be in the release. Thanks, Amonida -- Amonida Zadissa Ensembl Production team EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom From dstaines at ebi.ac.uk Tue Apr 29 10:31:48 2014 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 29 Apr 2014 10:31:48 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 23 Intentions Message-ID: <535F7184.8070500@ebi.ac.uk> Dear all, Release 23 of Ensembl Genomes is scheduled for 29th July 2014 - our intentions for this release can be found here: http://ensemblgenomes.org/info/release/23 Please note these are intentions and are therefore not guaranteed to be completed for July. Best regards, Dan Staines, on behalf of the Ensembl Genomes team. -- Dan Staines, PhD Technical Coordinator, Ensembl Genomes European Bioinformatics Institute (EMBL-EBI) http://www.ebi.ac.uk/ http://www.ensemblgenomes.org/ From denise at ebi.ac.uk Mon Apr 7 15:53:36 2014 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Mon, 7 Apr 2014 15:53:36 +0100 Subject: [ensembl-announce] Ensembl Genomes release 22 is out! Message-ID: <03E621CE-53FD-4913-8453-6EE11D6387CE@ebi.ac.uk> Dear all, We are delighted to announce that the latest update of Ensembl Genomes has been released. The highlights of release 22 are: New Genomes Ensembl Plants Amborella trichopoda Prunus persica (peach) Oryza (rice) genomes: O. barthii, O. glumaepatula, O. meridionalis, O. nivara, and O. punctate Ensembl Protists Bigelowiella natans Pythium (plant pathogens) genomes: P. aphanidermatum, P. arrhenomanes, P. irregulare, P. iwayamai, P. ultimum, and P. vexans Ensembl Metazoa Onchocerca volvulus Ensembl Bacteria 1,246 additional genomes (11,010 genomes now represented in total) New data Ensembl Plants Sorghum bicolor variation data based on the SAP panel (Morris et. al. 2013) Homoeologous genes between the wheat component A, B and D genomes Whole genome alignments Inter-homoleogue alignments between the wheat A, B and D genomes, and integration with the gene trees Between Amborella trichopoda and Arabidopsis thaliana, and Amborella trichopoda and Oriza sativa Japonica Between the five new rice genomes and O. sativa Japonica, as well as against each other new rice genome Updated data Ensembl Fungi Latest annotations for S. pombe from PomBase GO annotation projected from S cerevisiae and S pombe to all species Ensembl Metazoa Latest EST-based genes for many species Removal of haplotype regions in Anopheles gambiae Peptide comparative genomes Ensembl Plants Updated UniGene alignments in T. aestivum against its progenitors Peptide comparative genomes Questions or comments? Drop us a line at helpdesk at ensemblgenomes.org The Ensembl Genomes team -------------- next part -------------- An HTML attachment was scrubbed... URL: From rhoda at ebi.ac.uk Mon Apr 7 16:20:30 2014 From: rhoda at ebi.ac.uk (Rhoda Kinsella) Date: Mon, 7 Apr 2014 16:20:30 +0100 Subject: [ensembl-announce] Ensembl Pre! site with new Human GRCh38, Amazon molly, crab-eating macaque and hedgehog now available! Message-ID: Dear all, We are pleased to announce that the initial annotation of the new human assembly, GRCh38, is now live on Ensembl Pre! http://pre.ensembl.org/Homo_sapiens/Info/Index/ Highlights of GRCh38 Pre! include: Preliminary gene set including annotation on alternative loci (e.g. MHC haplotypes, LRC region) Centromeres covering 2% of the genome GENCODE 19 models mapped from e!75 (i.e. from GRCh37) CCDS models mapped from e!75 RefSeq annotation release 106 models Human-specific cDNA and EST alignments Computed consequences of variants overlapping an Ensembl transcript using the projected Ensembl gene set (Download GVF and VCF files from Pre! FTP site) Computed consequences for variants overlapping NCBI?s RefSeq transcripts (Download GVF and VCF files from Pre! FTP site) Pre! site has been updated to use Solr search In addition to human we're pleased to announce that we also have Pre! sites available for amazon molly, crab-eating macaque and hedgehog. Keep an eye out for further GRCh38 annotation updates by checking the blog category GRCh38. The Ensembl Pre! blog post with details about the GRCh38 annotation can be viewed here: http://www.ensembl.info/blog/2014/04/07/pre-site-for-the-new-human-assembly-grch38-is-live/ We'll be running a free 20 minute webinar about the data on Ensembl Pre! on Wed 16 April at 4PM BST. To register, click on the following link: https://attendee.gototraining.com/r/8084872084204567809 Regards, Rhoda Rhoda Kinsella Ph.D. Ensembl Production Project Leader European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD -------------- next part -------------- An HTML attachment was scrubbed... URL: From gspudich at ebi.ac.uk Tue Apr 15 11:06:11 2014 From: gspudich at ebi.ac.uk (Giulietta) Date: Tue, 15 Apr 2014 11:06:11 +0100 Subject: [ensembl-announce] Free Ensembl Webinar on Pre! - Human GRCh38, Amazon molly, crab-eating macaque and hedgehog In-Reply-To: <13CBDE6A-95BE-43D6-AE01-79BDCDF1B06A@ebi.ac.uk> References: <13CBDE6A-95BE-43D6-AE01-79BDCDF1B06A@ebi.ac.uk> Message-ID: <534D0493.7080408@ebi.ac.uk> Reminder: we offer a free 20 minute webinar tomorrow (Wednesday, 4PM BST) on what's available on Pre! Sign up here: https://attendee.gototraining.com/r/8084872084204567809 Best wishes, Ensembl Outreach On 07/04/2014 16:20, Rhoda Kinsella wrote: > Dear all, > We are pleased to announce that the initial annotation of the new > human assembly, GRCh38, is now live on Ensembl Pre! > http://pre.ensembl.org/Homo_sapiens/Info/Index/ > > > *Highlights of GRCh38 Pre! include:* > > * Preliminary gene set including annotation on alternative loci > (e.g. MHC haplotypes, LRC region) > * Centromeres covering 2% of the genome > * GENCODE 19 models mapped from e!75 (i.e. from GRCh37) > * CCDS models mapped from e!75 > * RefSeq annotation release 106 models > * Human-specific cDNA and EST alignments > * Computed consequences of variants overlapping an Ensembl > transcript using the projected Ensembl gene set (Download GVF and > VCF files from Pre! FTP site ) > * Computed consequences for variants overlapping NCBI's RefSeq > transcripts (Download GVF and VCF files from Pre! FTP site > ) > * Pre! site has been updated to use Solr search > > > In addition to human we're pleased to announce that we also have Pre! > sites available for a > mazon molly > , crab-eating > macaque and > hedgehog . > > Keep an eye out for further GRCh38 annotation updates by checking the > blog category GRCh38 > . > > The Ensembl Pre! blog post with details about the GRCh38 annotation > can be viewed here: > http://www.ensembl.info/blog/2014/04/07/pre-site-for-the-new-human-assembly-grch38-is-live/ > > We'll be running a free 20 minute webinar about the data on Ensembl > Pre! on Wed 16 April at 4PM BST. To register, click on the following > link: https://attendee.gototraining.com/r/8084872084204567809 > > Regards, > Rhoda > > > Rhoda Kinsella Ph.D. > Ensembl Production Project Leader > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Trust Genome Campus > Hinxton, > Cambridge > CB10 1SD > > > > > > > _______________________________________________ > Ensembl-campus mailing list > Ensembl-campus at ebi.ac.uk > http://listserver.ebi.ac.uk/mailman/listinfo/ensembl-campus -------------- next part -------------- An HTML attachment was scrubbed... URL: From amonida at ebi.ac.uk Wed Apr 23 10:17:47 2014 From: amonida at ebi.ac.uk (Amonida Zadissa) Date: Wed, 23 Apr 2014 10:17:47 +0100 Subject: [ensembl-announce] Declarations of intentions for Ensembl release 76 Message-ID: <5357853B.2030900@ebi.ac.uk> Dear all, Please find the summary of the declarations of intentions for Ensembl release 76 (scheduled for the 24th of July 2014) on our public website: http://admin.ensembl.org/Changelog/Summary Note these are intentions and are not guaranteed to be in the release. Thanks, Amonida -- Amonida Zadissa Ensembl Production team EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom From dstaines at ebi.ac.uk Tue Apr 29 10:31:48 2014 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 29 Apr 2014 10:31:48 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 23 Intentions Message-ID: <535F7184.8070500@ebi.ac.uk> Dear all, Release 23 of Ensembl Genomes is scheduled for 29th July 2014 - our intentions for this release can be found here: http://ensemblgenomes.org/info/release/23 Please note these are intentions and are therefore not guaranteed to be completed for July. Best regards, Dan Staines, on behalf of the Ensembl Genomes team. -- Dan Staines, PhD Technical Coordinator, Ensembl Genomes European Bioinformatics Institute (EMBL-EBI) http://www.ebi.ac.uk/ http://www.ensemblgenomes.org/