From maurel at ebi.ac.uk Thu Aug 7 10:42:36 2014 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Thu, 7 Aug 2014 10:42:36 +0100 Subject: [ensembl-announce] Ensembl release 76 is out! Message-ID: We are pleased to announce that the latest Ensembl update (e!76) has been released: http://www.ensembl.org/ Highlights of this release include: Updated human assembly to GRCh38 (GENCODE 20) Updated mouse gene set (GENCODE M3) New BLAST/BLAT New regulation displays New species: Amazon molly and Olive baboon Improved sequence export Imported the latest sequence variants from dbSNP build 140 for chicken, cow, pig and sheep. A complete list of the changes in release 76 can be found at http://www.ensembl.org/info/website/news.html For the latest news from the Ensembl project visit our blog at http://www.ensembl.info The release 76 blog post can be viewed here: http://www.ensembl.info/blog/2014/08/07/ensembl-76-has-been-released/ Best Regards, Thomas -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: From gspudich at ebi.ac.uk Mon Aug 11 16:10:02 2014 From: gspudich at ebi.ac.uk (Giulietta) Date: Mon, 11 Aug 2014 16:10:02 +0100 Subject: [ensembl-announce] Free Ensembl Webinars: e76 and the New Human Assembly In-Reply-To: <53E38E8A.2010309@ebi.ac.uk> References: <53E38E8A.2010309@ebi.ac.uk> Message-ID: <53E8DCCA.9010305@ebi.ac.uk> *Dear all,* *What's New?* Would you like to know more about the new Ensembl release? e76 provides access to the new human assembly along with high quality annotation including new regulatory regions (sequences that may be involved in gene regulation) and a new BLAST/BLAT tool. Two species (Amazon molly and Olive baboon) are released with full gene sets to add to the 60+ species in our main site. *Free Webinar ...* Find out all about it in Ensembl's Release Webinar e76 (Wed, August 20, 2014 4:00 PM - 4.30 PM GMT). Register for free here:http://tinyurl.com/e76-webinar *Coming soon ...* In September, we will discuss the new human assembly (GRCh38) along with the GRC. Register for free to our joint webinar (Wed, September 17, 2014 4:00 PM -- 4:30 PM GMT) http://tinyurl.com/GRCh38-webinar Best wishes, The Ensembl Team -- Mailing lists: www.ensembl.org/info/about/contact/mailing.html Blog: www.ensembl.info YouTube: www.youtube.com/user/EnsemblHelpdesk Online course: www.ensembl.info/ecourse Facebook: www.facebook.com/Ensembl.org Twitter: twitter.com/Ensembl -------------- next part -------------- An HTML attachment was scrubbed... URL: From maurel at ebi.ac.uk Tue Aug 12 09:36:07 2014 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Tue, 12 Aug 2014 09:36:07 +0100 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 77 Message-ID: Dear all, Please find the summary of the declarations of intentions for Ensembl release 77 (scheduled for the 1st of October 2014) on our public website: http://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) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: From denise at ebi.ac.uk Tue Aug 19 11:38:42 2014 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Tue, 19 Aug 2014 11:38:42 +0100 Subject: [ensembl-announce] New Ensembl Genomes release is out! Message-ID: <94925a11787df9c2576a041123a6de18.squirrel@webmail.ebi.ac.uk> Dear all, We have just released the latest update of Ensembl Genomes. The highlights of release 23 are: New Genomes Ensembl Plants ? Theobroma cacao ? Oryza rufipogon ? Brassica oleracea ? Ostreococcus lucimarinus ? Leersia perrieri Ensembl Fungi Seven additional plant pathogens: ? Colletotrichum genomes: C. gloeosporioides, C. higginsianum, C. orbiculare ? Dothistroma septosporum ? Fusarium fujikuroi ? Fusarium pseudograminearum ? Pussinia graminis Ug99 Ensembl Protists ? Phytophthora genomes: P. kernovia, P. lateralis and P. parasitica Ensembl Metazoa ? Melitaea cinxia ? Mnemiopsis leidyi, the first ctenophore to be sequenced! Ensembl Bacteria ? > 4K new genomes: 15,944 genomes now represented in total New Data Ensembl Metazoa ? Variation data: Aedes aegypti ? Annotation: Strongylocentrotus purpuratus (gene models based on transcriptomic data) ? ncRNA annotation is now available for several species Ensembl Protists ? DNA alignments: Pythium sp and Phytophthora sp Ensembl Plants ? Variation data: Zea mays, Sorghum bicolor and Triticum aestivum Alignments ? Triticum aestivum: transcriptomic and whole genome In addition to New Genomes and New Data, BioMarts, gene trees and comparative genomics have been updated in this new release. A complete list of the changes can be found on the Ensembl Genomes website: www.ensemblgenomes.org Have fun with the new release and get in touch if you have any questions. The Ensembl Genomes team. From dstaines at ebi.ac.uk Wed Aug 20 15:12:03 2014 From: dstaines at ebi.ac.uk (Dan Staines) Date: Wed, 20 Aug 2014 15:12:03 +0100 Subject: [ensembl-announce] New Ensembl Genomes REST server Message-ID: <53F4ACB3.2000007@ebi.ac.uk> The REST server provided by Ensembl Genomes has now been updated to use the latest v3.0.0 codebase provided by Ensembl, plus supplementary endpoints for genome discovery and bacterial family/genome retrieval. For more information on these additional endpoints, please visit: https://github.com/EnsemblGenomes/eg-rest/wiki/ The new server is available at http://rest.ensemblgenomes.org/ - please note that http://beta.ensemblgenomes.org will remain accessible until the next release of Ensembl Genomes in October after which point it will be removed. Thanks, Dan. -- Dan Staines, PhD Technical Coordinator, Ensembl Genomes European Bioinformatics Institute (EMBL-EBI) http://www.ebi.ac.uk/ http://www.ensemblgenomes.org/ From dstaines at ebi.ac.uk Fri Aug 22 12:28:52 2014 From: dstaines at ebi.ac.uk (Dan Staines) Date: Fri, 22 Aug 2014 12:28:52 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 24 Intentions Message-ID: <53F72974.4020400@ebi.ac.uk> Dear all, Release 24 of Ensembl Genomes is scheduled for 14th October 2014 - our intentions for this release can be found here: http://ensemblgenomes.org/info/release/24 Please note these are intentions and are therefore not guaranteed to be completed for October. 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 maurel at ebi.ac.uk Thu Aug 7 10:42:36 2014 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Thu, 7 Aug 2014 10:42:36 +0100 Subject: [ensembl-announce] Ensembl release 76 is out! Message-ID: We are pleased to announce that the latest Ensembl update (e!76) has been released: http://www.ensembl.org/ Highlights of this release include: Updated human assembly to GRCh38 (GENCODE 20) Updated mouse gene set (GENCODE M3) New BLAST/BLAT New regulation displays New species: Amazon molly and Olive baboon Improved sequence export Imported the latest sequence variants from dbSNP build 140 for chicken, cow, pig and sheep. A complete list of the changes in release 76 can be found at http://www.ensembl.org/info/website/news.html For the latest news from the Ensembl project visit our blog at http://www.ensembl.info The release 76 blog post can be viewed here: http://www.ensembl.info/blog/2014/08/07/ensembl-76-has-been-released/ Best Regards, Thomas -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: From gspudich at ebi.ac.uk Mon Aug 11 16:10:02 2014 From: gspudich at ebi.ac.uk (Giulietta) Date: Mon, 11 Aug 2014 16:10:02 +0100 Subject: [ensembl-announce] Free Ensembl Webinars: e76 and the New Human Assembly In-Reply-To: <53E38E8A.2010309@ebi.ac.uk> References: <53E38E8A.2010309@ebi.ac.uk> Message-ID: <53E8DCCA.9010305@ebi.ac.uk> *Dear all,* *What's New?* Would you like to know more about the new Ensembl release? e76 provides access to the new human assembly along with high quality annotation including new regulatory regions (sequences that may be involved in gene regulation) and a new BLAST/BLAT tool. Two species (Amazon molly and Olive baboon) are released with full gene sets to add to the 60+ species in our main site. *Free Webinar ...* Find out all about it in Ensembl's Release Webinar e76 (Wed, August 20, 2014 4:00 PM - 4.30 PM GMT). Register for free here:http://tinyurl.com/e76-webinar *Coming soon ...* In September, we will discuss the new human assembly (GRCh38) along with the GRC. Register for free to our joint webinar (Wed, September 17, 2014 4:00 PM -- 4:30 PM GMT) http://tinyurl.com/GRCh38-webinar Best wishes, The Ensembl Team -- Mailing lists: www.ensembl.org/info/about/contact/mailing.html Blog: www.ensembl.info YouTube: www.youtube.com/user/EnsemblHelpdesk Online course: www.ensembl.info/ecourse Facebook: www.facebook.com/Ensembl.org Twitter: twitter.com/Ensembl -------------- next part -------------- An HTML attachment was scrubbed... URL: From maurel at ebi.ac.uk Tue Aug 12 09:36:07 2014 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Tue, 12 Aug 2014 09:36:07 +0100 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 77 Message-ID: Dear all, Please find the summary of the declarations of intentions for Ensembl release 77 (scheduled for the 1st of October 2014) on our public website: http://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) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: From denise at ebi.ac.uk Tue Aug 19 11:38:42 2014 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Tue, 19 Aug 2014 11:38:42 +0100 Subject: [ensembl-announce] New Ensembl Genomes release is out! Message-ID: <94925a11787df9c2576a041123a6de18.squirrel@webmail.ebi.ac.uk> Dear all, We have just released the latest update of Ensembl Genomes. The highlights of release 23 are: New Genomes Ensembl Plants ? Theobroma cacao ? Oryza rufipogon ? Brassica oleracea ? Ostreococcus lucimarinus ? Leersia perrieri Ensembl Fungi Seven additional plant pathogens: ? Colletotrichum genomes: C. gloeosporioides, C. higginsianum, C. orbiculare ? Dothistroma septosporum ? Fusarium fujikuroi ? Fusarium pseudograminearum ? Pussinia graminis Ug99 Ensembl Protists ? Phytophthora genomes: P. kernovia, P. lateralis and P. parasitica Ensembl Metazoa ? Melitaea cinxia ? Mnemiopsis leidyi, the first ctenophore to be sequenced! Ensembl Bacteria ? > 4K new genomes: 15,944 genomes now represented in total New Data Ensembl Metazoa ? Variation data: Aedes aegypti ? Annotation: Strongylocentrotus purpuratus (gene models based on transcriptomic data) ? ncRNA annotation is now available for several species Ensembl Protists ? DNA alignments: Pythium sp and Phytophthora sp Ensembl Plants ? Variation data: Zea mays, Sorghum bicolor and Triticum aestivum Alignments ? Triticum aestivum: transcriptomic and whole genome In addition to New Genomes and New Data, BioMarts, gene trees and comparative genomics have been updated in this new release. A complete list of the changes can be found on the Ensembl Genomes website: www.ensemblgenomes.org Have fun with the new release and get in touch if you have any questions. The Ensembl Genomes team. From dstaines at ebi.ac.uk Wed Aug 20 15:12:03 2014 From: dstaines at ebi.ac.uk (Dan Staines) Date: Wed, 20 Aug 2014 15:12:03 +0100 Subject: [ensembl-announce] New Ensembl Genomes REST server Message-ID: <53F4ACB3.2000007@ebi.ac.uk> The REST server provided by Ensembl Genomes has now been updated to use the latest v3.0.0 codebase provided by Ensembl, plus supplementary endpoints for genome discovery and bacterial family/genome retrieval. For more information on these additional endpoints, please visit: https://github.com/EnsemblGenomes/eg-rest/wiki/ The new server is available at http://rest.ensemblgenomes.org/ - please note that http://beta.ensemblgenomes.org will remain accessible until the next release of Ensembl Genomes in October after which point it will be removed. Thanks, Dan. -- Dan Staines, PhD Technical Coordinator, Ensembl Genomes European Bioinformatics Institute (EMBL-EBI) http://www.ebi.ac.uk/ http://www.ensemblgenomes.org/ From dstaines at ebi.ac.uk Fri Aug 22 12:28:52 2014 From: dstaines at ebi.ac.uk (Dan Staines) Date: Fri, 22 Aug 2014 12:28:52 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 24 Intentions Message-ID: <53F72974.4020400@ebi.ac.uk> Dear all, Release 24 of Ensembl Genomes is scheduled for 14th October 2014 - our intentions for this release can be found here: http://ensemblgenomes.org/info/release/24 Please note these are intentions and are therefore not guaranteed to be completed for October. 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/