From maurel at ebi.ac.uk Thu Apr 11 10:32:43 2013 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Thu, 11 Apr 2013 10:32:43 +0100 Subject: [ensembl-announce] Ensembl release 71 is out! Message-ID: <25B2A92D-F4BF-4236-A3FF-70696B64D9C1@ebi.ac.uk> We are pleased to announce that the latest Ensembl update (e!71) has been released : http://www.ensembl.org/ Highlights of this release include: Human: New ?clinically associated? summary track on Region in Detail for human variation, import of COSMIC version 63 and update of COSMIC structural variants. Other species: SIFT scores for all possible changes to the proteome in human, mouse, zebrafish, pig, cow, chicken, rat and dog. Updated gene sets for human and zebrafish with manual annotation from HAVANA. Updated gene set for anole lizard, including RNAseq data. New assemblies for chicken (Galgal4) and C. elegans (WBcel235). Other news: New expression view to the set of gene-based displays, listing the available RNASeq data for a given species. A new transcript comparison view allows comparison of transcript sequences for a gene. A scrollable overview panel (supported by most updated browsers) is now available on the Region in detail view. A complete list of the changes in release 71 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 blog post can be viewed here: http://www.ensembl.info/blog/2013/04/11/ensembl-71-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 dstaines at ebi.ac.uk Thu Apr 18 09:45:28 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 18 Apr 2013 09:45:28 +0100 Subject: [ensembl-announce] [ensembl-dev] Ensembl Genomes Release 18 In-Reply-To: <51225DCB.1040602@ebi.ac.uk> References: <51225DCB.1040602@ebi.ac.uk> Message-ID: <516FB2A8.600@ebi.ac.uk> Dear all, We now anticipate the release of Ensembl Genomes 18 by Thursday 25th April. We apologise for any inconvenience caused. 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 dstaines at ebi.ac.uk Thu Apr 18 14:50:52 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 18 Apr 2013 09:50:52 -0400 Subject: [ensembl-announce] [ensembl-dev] Ensembl Genomes Release 18 In-Reply-To: <51225DCB.1040602@ebi.ac.uk> References: <51225DCB.1040602@ebi.ac.uk> Message-ID: <604F96C5C847438DA3B273FE030A3078@buad.bloomu.edu> Dear all, We now anticipate the release of Ensembl Genomes 18 by Thursday 25th April. We apologise for any inconvenience caused. 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/ _______________________________________________ Dev mailing list Dev at ensembl.org Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev Ensembl Blog: http://www.ensembl.info/ From maurel at ebi.ac.uk Mon Apr 22 10:51:44 2013 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Mon, 22 Apr 2013 10:51:44 +0100 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 72 Message-ID: Dear all, Please find the summary of the declarations of intentions for Ensembl release 72 (scheduled for the 11th of June 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 Apr 26 14:09:35 2013 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Fri, 26 Apr 2013 14:09:35 +0100 Subject: [ensembl-announce] Ensembl Genomes 18 has been released! Message-ID: <72CBC0AB-A580-4837-AC06-AC4C438E55D7@ebi.ac.uk> Dear all, The Ensembl Genomes project has celebrated its 4th year anniversary in the beginning of this week and now we are pleased to announce another milestone: Ensembl Genomes release 18. In our latest release, we provide several new species for all divisions of Ensembl Genomes, which includes three new genomes in Ensembl Fungi (Yarrowia lipolytica, Cryptococcus neoformans and Trichoderma reesei); one new genome in Ensembl Protists (Guillardia theta); four new genomes in Ensembl Metazoa (Brugia malayi, Loa loa, Megaselia scalaris and Strigamia maritima); one new species in Ensembl Plants (Medicago truncatula). We have also incorporated the latest versions of prokaryotic genomes from INSDC in Ensembl Bacteria. NOTE: The updated public mysql database will be available on Monday, April 29th 2013. The detailed features of this new release are: * Bacteria ? Addition of cross-references to Rhea in Ensembl Bacteria; ? New and updated genomes: 6,305 bacterial genomes in total, all deposited in ENA. * Fungi ? Three new species are included in Ensembl Fungi: the human pathogen Cryptococcus neoformans, and the industrially important species Yarrowia lipolytica and Trichoderma reesei; ? New Botryotinia fuckeliana assembly and EST data; ? Updated annotation for Schizosaccharomyces pombe from PomBase. * Protists ? Extended taxonomic coverage with the newly added Guillardia theta genome; ? Updated DNA alignments and synteny for tramenopiles genomes. * Metazoa ? Two new parasitic nematode genomes: Brugia malayi (causative agent of lymphatic filariasis) and Loa loa (causative agent of subcutaneous filariasis); ? The genomes of scuttle fly (Megaselia scalaris) and the centipede Strigamia maritima are now available. The latter is the first myriapod genome to be included in Ensembl Metazoa; ? Updated assembly for Caenorhabditis elegans and Schistosoma mansoni. * Plants ? Barrel clover (Medicago truncatula) is now available. This is the second legume genome to be included in Ensembl Plants; ? New visualization of barley (Hordeum vulgare) physical map anchoring the gene space assembly; ? Whole genome alignments between barley, rice and brachypodium; ? Updated maize (Zea mays) assembly to version 3; ? New variation datasets for barley and Brachypodium distachyon; ? Alignments of Triticum aestivum (bread wheat) WGS, TSA and EST assemblies against the barley genome are now available. The bread wheat data can also still be visualised in the context ofBracypodium distachyon; ? Protein domain predictions and cross references have been updated for most plant genomes; ? New pairwise alignments between several genome sequences. * Software migration to Ensembl 71 Have fun! The Ensembl Genomes Team From dstaines at ebi.ac.uk Tue Apr 30 10:22:29 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 30 Apr 2013 10:22:29 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 19 Intentions Message-ID: <517F8D55.4030601@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 19 of Ensembl Genomes, due out on 2nd July 2013. Please note these are intentions and are therefore not guaranteed to be completed for July. These can also be viewed online at: http://ensemblgenomes.org/info/release19 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. General - Release scheduled for 2nd July 2013 - Update to Ensembl 72 software - Update of pan homology comparative genomics database to include latest versions of genomes from Ensembl and Ensembl Genomes, including the addition of: -- Tetranychus urticae -- Lottia gigantea -- Helobdella robusta Bacteria - New and updated genomes -- Updated to reflect latest genome set available from INSDC - Updated data -- Updated gene families database -- Addition of MetaCyc cross-references -- Full representation of assembly structure Fungi - Updated genomes -- Updated S. pombe gene models and new annotations - New data -- New Phytopath Annotations -- RNA-Seq for Zymoseptoria tritici Protists - New genomes -- Paramecium tetraurelia (Ciliate) - New data -- DNA alignment for Ciliates -- Updated data -- Peptide compara -- Biomart Metazoa - New genomes -- Rhodnius prolixus (a hemipteran, imported from VectorBase) -- Tetranychus urticae (red spider mite, a chelicerate) -- Crassostrea gigas (Pacific oyster) -- Lottia gigantea (owl limpet) -- Capitella teleta (polychaete worm, an annelid) -- Helobdella robusta (leech, another annelid worm) - Updated data -- Peptide comparative genomics -- BioMart Plants - New genomes -- Triticum urartu (wheat A-genome progenitor) -- Aegilops tauschii (wheat D-genome) - New data -- New sorghum variations -- New tomato variations -- New probe mappings for potato and tomato -- New R-gene data for potato - Updated data -- Revised barley variations -- DNA and Peptide compara -- 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 Thu Apr 11 10:32:43 2013 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Thu, 11 Apr 2013 10:32:43 +0100 Subject: [ensembl-announce] Ensembl release 71 is out! Message-ID: <25B2A92D-F4BF-4236-A3FF-70696B64D9C1@ebi.ac.uk> We are pleased to announce that the latest Ensembl update (e!71) has been released : http://www.ensembl.org/ Highlights of this release include: Human: New ?clinically associated? summary track on Region in Detail for human variation, import of COSMIC version 63 and update of COSMIC structural variants. Other species: SIFT scores for all possible changes to the proteome in human, mouse, zebrafish, pig, cow, chicken, rat and dog. Updated gene sets for human and zebrafish with manual annotation from HAVANA. Updated gene set for anole lizard, including RNAseq data. New assemblies for chicken (Galgal4) and C. elegans (WBcel235). Other news: New expression view to the set of gene-based displays, listing the available RNASeq data for a given species. A new transcript comparison view allows comparison of transcript sequences for a gene. A scrollable overview panel (supported by most updated browsers) is now available on the Region in detail view. A complete list of the changes in release 71 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 blog post can be viewed here: http://www.ensembl.info/blog/2013/04/11/ensembl-71-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 dstaines at ebi.ac.uk Thu Apr 18 09:45:28 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 18 Apr 2013 09:45:28 +0100 Subject: [ensembl-announce] [ensembl-dev] Ensembl Genomes Release 18 In-Reply-To: <51225DCB.1040602@ebi.ac.uk> References: <51225DCB.1040602@ebi.ac.uk> Message-ID: <516FB2A8.600@ebi.ac.uk> Dear all, We now anticipate the release of Ensembl Genomes 18 by Thursday 25th April. We apologise for any inconvenience caused. 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 dstaines at ebi.ac.uk Thu Apr 18 14:50:52 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 18 Apr 2013 09:50:52 -0400 Subject: [ensembl-announce] [ensembl-dev] Ensembl Genomes Release 18 In-Reply-To: <51225DCB.1040602@ebi.ac.uk> References: <51225DCB.1040602@ebi.ac.uk> Message-ID: <604F96C5C847438DA3B273FE030A3078@buad.bloomu.edu> Dear all, We now anticipate the release of Ensembl Genomes 18 by Thursday 25th April. We apologise for any inconvenience caused. 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/ _______________________________________________ Dev mailing list Dev at ensembl.org Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev Ensembl Blog: http://www.ensembl.info/ From maurel at ebi.ac.uk Mon Apr 22 10:51:44 2013 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Mon, 22 Apr 2013 10:51:44 +0100 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 72 Message-ID: Dear all, Please find the summary of the declarations of intentions for Ensembl release 72 (scheduled for the 11th of June 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 Apr 26 14:09:35 2013 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Fri, 26 Apr 2013 14:09:35 +0100 Subject: [ensembl-announce] Ensembl Genomes 18 has been released! Message-ID: <72CBC0AB-A580-4837-AC06-AC4C438E55D7@ebi.ac.uk> Dear all, The Ensembl Genomes project has celebrated its 4th year anniversary in the beginning of this week and now we are pleased to announce another milestone: Ensembl Genomes release 18. In our latest release, we provide several new species for all divisions of Ensembl Genomes, which includes three new genomes in Ensembl Fungi (Yarrowia lipolytica, Cryptococcus neoformans and Trichoderma reesei); one new genome in Ensembl Protists (Guillardia theta); four new genomes in Ensembl Metazoa (Brugia malayi, Loa loa, Megaselia scalaris and Strigamia maritima); one new species in Ensembl Plants (Medicago truncatula). We have also incorporated the latest versions of prokaryotic genomes from INSDC in Ensembl Bacteria. NOTE: The updated public mysql database will be available on Monday, April 29th 2013. The detailed features of this new release are: * Bacteria ? Addition of cross-references to Rhea in Ensembl Bacteria; ? New and updated genomes: 6,305 bacterial genomes in total, all deposited in ENA. * Fungi ? Three new species are included in Ensembl Fungi: the human pathogen Cryptococcus neoformans, and the industrially important species Yarrowia lipolytica and Trichoderma reesei; ? New Botryotinia fuckeliana assembly and EST data; ? Updated annotation for Schizosaccharomyces pombe from PomBase. * Protists ? Extended taxonomic coverage with the newly added Guillardia theta genome; ? Updated DNA alignments and synteny for tramenopiles genomes. * Metazoa ? Two new parasitic nematode genomes: Brugia malayi (causative agent of lymphatic filariasis) and Loa loa (causative agent of subcutaneous filariasis); ? The genomes of scuttle fly (Megaselia scalaris) and the centipede Strigamia maritima are now available. The latter is the first myriapod genome to be included in Ensembl Metazoa; ? Updated assembly for Caenorhabditis elegans and Schistosoma mansoni. * Plants ? Barrel clover (Medicago truncatula) is now available. This is the second legume genome to be included in Ensembl Plants; ? New visualization of barley (Hordeum vulgare) physical map anchoring the gene space assembly; ? Whole genome alignments between barley, rice and brachypodium; ? Updated maize (Zea mays) assembly to version 3; ? New variation datasets for barley and Brachypodium distachyon; ? Alignments of Triticum aestivum (bread wheat) WGS, TSA and EST assemblies against the barley genome are now available. The bread wheat data can also still be visualised in the context ofBracypodium distachyon; ? Protein domain predictions and cross references have been updated for most plant genomes; ? New pairwise alignments between several genome sequences. * Software migration to Ensembl 71 Have fun! The Ensembl Genomes Team From dstaines at ebi.ac.uk Tue Apr 30 10:22:29 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 30 Apr 2013 10:22:29 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 19 Intentions Message-ID: <517F8D55.4030601@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 19 of Ensembl Genomes, due out on 2nd July 2013. Please note these are intentions and are therefore not guaranteed to be completed for July. These can also be viewed online at: http://ensemblgenomes.org/info/release19 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. General - Release scheduled for 2nd July 2013 - Update to Ensembl 72 software - Update of pan homology comparative genomics database to include latest versions of genomes from Ensembl and Ensembl Genomes, including the addition of: -- Tetranychus urticae -- Lottia gigantea -- Helobdella robusta Bacteria - New and updated genomes -- Updated to reflect latest genome set available from INSDC - Updated data -- Updated gene families database -- Addition of MetaCyc cross-references -- Full representation of assembly structure Fungi - Updated genomes -- Updated S. pombe gene models and new annotations - New data -- New Phytopath Annotations -- RNA-Seq for Zymoseptoria tritici Protists - New genomes -- Paramecium tetraurelia (Ciliate) - New data -- DNA alignment for Ciliates -- Updated data -- Peptide compara -- Biomart Metazoa - New genomes -- Rhodnius prolixus (a hemipteran, imported from VectorBase) -- Tetranychus urticae (red spider mite, a chelicerate) -- Crassostrea gigas (Pacific oyster) -- Lottia gigantea (owl limpet) -- Capitella teleta (polychaete worm, an annelid) -- Helobdella robusta (leech, another annelid worm) - Updated data -- Peptide comparative genomics -- BioMart Plants - New genomes -- Triticum urartu (wheat A-genome progenitor) -- Aegilops tauschii (wheat D-genome) - New data -- New sorghum variations -- New tomato variations -- New probe mappings for potato and tomato -- New R-gene data for potato - Updated data -- Revised barley variations -- DNA and Peptide compara -- 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/