From jeff at ebi.ac.uk Wed Dec 1 11:54:06 2010 From: jeff at ebi.ac.uk (jeff at ebi.ac.uk) Date: Wed, 1 Dec 2010 11:54:06 -0000 (UTC) Subject: [ensembl-announce] Ensembl Genomes Release 7 Message-ID: <35383.86.14.238.218.1291204446.squirrel@webmail.ebi.ac.uk> The Ensembl Genomes Project is pleased to announce release 7 of Ensembl Genomes (http://www.ensemblgenomes.org/). The main highlights of this release are: * Software migration to Ensembl 60 * 66 new genomes added for Ensembl Bacteria and updated functional genomics databases for Escherichia/Shigella and Staphylococcus * Puccinia graminis f sp tritic genome added to Ensembl Fungi * Zea mays and Physcomitrella patens genomes added to Ensembl Plants, new variation datasets for Oryza sativa and updates to the functional genomics databases for Oryza sativa indica, Oryza sativa japonica and Arabidopsis thaliana * Acyrthosiphon pisum genome added to Ensembl Metazoa Please see the individual homepages for more detailed information: http://bacteria.ensembl.org http://protists.ensembl.org http://fungi.ensembl.org http://plants.ensembl.org http://metazoa.ensembl.org From dstaines at ebi.ac.uk Thu Dec 2 14:08:41 2010 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 02 Dec 2010 14:08:41 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 8 Intentions Message-ID: <4CF7A869.6090109@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 8 of Ensembl Genomes, due out on 8th February 2011. Please note these are intentions and are therefore not guaranteed to be completed for February. These can also be viewed online at: http://ensemblgenomes.org/info/release8 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. Ensembl Genomes Release 8 Intentions ------------------------------------ General - release scheduled for 8th February 2011 - update to Ensembl 61 software - updated pan concern databases from Ensembl - new Pan Compara database comprising: -- a selection of vertebrate genomes from Ensembl 61 (now including Gasterosteus aculeatus) -- a selection of genomes from Ensembl Genomes 8 including the following new Ensembl Genomes species: --- Magnaporthe grisea --- Phytophora infestans --- Strongylocentrotus purpuratus --- Schistosoma mansoni --- Nematostella vectensis --- Trichoplax adhaerens --- Apis mellifera --- Bombyx mori --- Physcomitrella patens -- but no longer including: --- Plasmodium vivax --- Equus caballus --- Macaca mulatta Metazoa - core databases for the following new genomes: -- Strongylocentrotus purpuratus (Echinodermata) (sea urchin) -- Schistosoma mansoni (Platyhelminth) (blood fluke) -- Nematostella vectensis (Cnidaria) (sea anemone) -- Trichoplax adhaerens (Placozoa) -- Apis mellifera (Arthropoda) (honey bee) -- Bombyx mori (Arthropoda) (silk moth) - updated core database for Anopheles gambiae PEST - updated core database for Caenorhabditis elegans based on WormBase WS220 - updated cross-references for Anopheles, Aedes, Culex and Pediculus - updated peptide compara database - updated functional genomics database for Anopheles gambiae - updated variation database for Anopheles gambiae - updates to include UniParc accessions for all cores Protists - core databases for the following new oomycete genomes: -- Phytopthora infestans -- Phytopthora ramorum -- Phytopthora sojae - updates to include UniParc accessions for all cores - updated peptide compara database - updated DNA compara including pairwise comparisons between new Phytopthora - updated gene and sequence biomarts Fungi - core database for the new genome Magnaporthe grisea - minor update to gene models for 5 Aspergillus species - updates to include UniParc accessions for all cores - updated peptide compara database - updated gene and sequence biomarts Bacteria - patch for funcgen analyses - no other significant updates planned Plants - update to Arabidopsis thaliana variation to include substitution data from WTCHG - no other significant updates planned -- 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 ap5 at sanger.ac.uk Mon Dec 13 09:58:41 2010 From: ap5 at sanger.ac.uk (Anne Parker) Date: Mon, 13 Dec 2010 09:58:41 +0000 Subject: [ensembl-announce] BLAST databases - scheduled downtime Message-ID: <505CFCC7-EFF6-4540-8D19-6BB5EDC6A29E@sanger.ac.uk> Our BLAST databases are due for maintenance work, which has been scheduled for Wednesday 15th December, in the morning (UK time). Both the UK and US West sites will be affected, with BLAST being unavailable during this time; our apologies for any inconvenience caused. Regards Anne Anne Parker Ensembl Web Production Manager http://www.ensembl.org From ap5 at sanger.ac.uk Tue Dec 21 16:10:42 2010 From: ap5 at sanger.ac.uk (Anne Parker) Date: Tue, 21 Dec 2010 16:10:42 +0000 Subject: [ensembl-announce] BLAST maintenance Message-ID: <4A267A65-89D3-4027-BCE9-902E01EFC218@sanger.ac.uk> Hi all The routine maintenance of our BLAST databases has been rescheduled for tomorrow, Wednesday 22nd December, around 10am UK time. We will let you know when work is complete; please accept our apologies for any inconvenience caused. Regards Anne Anne Parker Ensembl Web Production Manager http://www.ensembl.org From ap5 at sanger.ac.uk Wed Dec 22 14:23:00 2010 From: ap5 at sanger.ac.uk (Anne Parker) Date: Wed, 22 Dec 2010 14:23:00 +0000 Subject: [ensembl-announce] Ensembl UK shutdown - 8/9th January 2011 Message-ID: <89CF7751-0E36-4D3D-8728-54F26595E89D@sanger.ac.uk> Hi all Owing to problems with our data centre cooling system, the Sanger network will be offline from around 4.30pm on Friday 7th January until the evening of Sunday 9th January (UK time). This means that all UK-based Ensembl sites, including www.ensembl.org, archives and pre site, will be unavailable from late Friday afternoon until Monday morning. Our US mirror sites will be available, but services that depend on machines based in the UK, i.e. BLAST/BLAT and user logins, will be disabled during this time. Please accept our apologies for any inconvenience caused. A reminder will be sent out nearer the time. Regards Anne Anne Parker Ensembl Web Production Manager http://www.ensembl.org From st3 at sanger.ac.uk Wed Dec 22 14:30:17 2010 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Wed, 22 Dec 2010 14:30:17 +0000 Subject: [ensembl-announce] BLAST maintenance In-Reply-To: <4A267A65-89D3-4027-BCE9-902E01EFC218@sanger.ac.uk> References: <4A267A65-89D3-4027-BCE9-902E01EFC218@sanger.ac.uk> Message-ID: <4D120B79.10000@sanger.ac.uk> The maintenance has been completed and BLAST is now back online. Regards, Steve On 12/21/10 16:10, Anne Parker wrote: > Hi all > > The routine maintenance of our BLAST databases has been rescheduled > for tomorrow, Wednesday 22nd December, around 10am UK time. We will > let you know when work is complete; please accept our apologies for > any inconvenience caused. > > Regards > > Anne > > > Anne Parker > Ensembl Web Production Manager > http://www.ensembl.org > > > > > _______________________________________________ > Announce mailing list > Announce at ensembl.org > http://lists.ensembl.org/mailman/listinfo/announce From jeff at ebi.ac.uk Wed Dec 1 11:54:06 2010 From: jeff at ebi.ac.uk (jeff at ebi.ac.uk) Date: Wed, 1 Dec 2010 11:54:06 -0000 (UTC) Subject: [ensembl-announce] Ensembl Genomes Release 7 Message-ID: <35383.86.14.238.218.1291204446.squirrel@webmail.ebi.ac.uk> The Ensembl Genomes Project is pleased to announce release 7 of Ensembl Genomes (http://www.ensemblgenomes.org/). The main highlights of this release are: * Software migration to Ensembl 60 * 66 new genomes added for Ensembl Bacteria and updated functional genomics databases for Escherichia/Shigella and Staphylococcus * Puccinia graminis f sp tritic genome added to Ensembl Fungi * Zea mays and Physcomitrella patens genomes added to Ensembl Plants, new variation datasets for Oryza sativa and updates to the functional genomics databases for Oryza sativa indica, Oryza sativa japonica and Arabidopsis thaliana * Acyrthosiphon pisum genome added to Ensembl Metazoa Please see the individual homepages for more detailed information: http://bacteria.ensembl.org http://protists.ensembl.org http://fungi.ensembl.org http://plants.ensembl.org http://metazoa.ensembl.org From dstaines at ebi.ac.uk Thu Dec 2 14:08:41 2010 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 02 Dec 2010 14:08:41 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 8 Intentions Message-ID: <4CF7A869.6090109@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 8 of Ensembl Genomes, due out on 8th February 2011. Please note these are intentions and are therefore not guaranteed to be completed for February. These can also be viewed online at: http://ensemblgenomes.org/info/release8 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. Ensembl Genomes Release 8 Intentions ------------------------------------ General - release scheduled for 8th February 2011 - update to Ensembl 61 software - updated pan concern databases from Ensembl - new Pan Compara database comprising: -- a selection of vertebrate genomes from Ensembl 61 (now including Gasterosteus aculeatus) -- a selection of genomes from Ensembl Genomes 8 including the following new Ensembl Genomes species: --- Magnaporthe grisea --- Phytophora infestans --- Strongylocentrotus purpuratus --- Schistosoma mansoni --- Nematostella vectensis --- Trichoplax adhaerens --- Apis mellifera --- Bombyx mori --- Physcomitrella patens -- but no longer including: --- Plasmodium vivax --- Equus caballus --- Macaca mulatta Metazoa - core databases for the following new genomes: -- Strongylocentrotus purpuratus (Echinodermata) (sea urchin) -- Schistosoma mansoni (Platyhelminth) (blood fluke) -- Nematostella vectensis (Cnidaria) (sea anemone) -- Trichoplax adhaerens (Placozoa) -- Apis mellifera (Arthropoda) (honey bee) -- Bombyx mori (Arthropoda) (silk moth) - updated core database for Anopheles gambiae PEST - updated core database for Caenorhabditis elegans based on WormBase WS220 - updated cross-references for Anopheles, Aedes, Culex and Pediculus - updated peptide compara database - updated functional genomics database for Anopheles gambiae - updated variation database for Anopheles gambiae - updates to include UniParc accessions for all cores Protists - core databases for the following new oomycete genomes: -- Phytopthora infestans -- Phytopthora ramorum -- Phytopthora sojae - updates to include UniParc accessions for all cores - updated peptide compara database - updated DNA compara including pairwise comparisons between new Phytopthora - updated gene and sequence biomarts Fungi - core database for the new genome Magnaporthe grisea - minor update to gene models for 5 Aspergillus species - updates to include UniParc accessions for all cores - updated peptide compara database - updated gene and sequence biomarts Bacteria - patch for funcgen analyses - no other significant updates planned Plants - update to Arabidopsis thaliana variation to include substitution data from WTCHG - no other significant updates planned -- 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 ap5 at sanger.ac.uk Mon Dec 13 09:58:41 2010 From: ap5 at sanger.ac.uk (Anne Parker) Date: Mon, 13 Dec 2010 09:58:41 +0000 Subject: [ensembl-announce] BLAST databases - scheduled downtime Message-ID: <505CFCC7-EFF6-4540-8D19-6BB5EDC6A29E@sanger.ac.uk> Our BLAST databases are due for maintenance work, which has been scheduled for Wednesday 15th December, in the morning (UK time). Both the UK and US West sites will be affected, with BLAST being unavailable during this time; our apologies for any inconvenience caused. Regards Anne Anne Parker Ensembl Web Production Manager http://www.ensembl.org From ap5 at sanger.ac.uk Tue Dec 21 16:10:42 2010 From: ap5 at sanger.ac.uk (Anne Parker) Date: Tue, 21 Dec 2010 16:10:42 +0000 Subject: [ensembl-announce] BLAST maintenance Message-ID: <4A267A65-89D3-4027-BCE9-902E01EFC218@sanger.ac.uk> Hi all The routine maintenance of our BLAST databases has been rescheduled for tomorrow, Wednesday 22nd December, around 10am UK time. We will let you know when work is complete; please accept our apologies for any inconvenience caused. Regards Anne Anne Parker Ensembl Web Production Manager http://www.ensembl.org From ap5 at sanger.ac.uk Wed Dec 22 14:23:00 2010 From: ap5 at sanger.ac.uk (Anne Parker) Date: Wed, 22 Dec 2010 14:23:00 +0000 Subject: [ensembl-announce] Ensembl UK shutdown - 8/9th January 2011 Message-ID: <89CF7751-0E36-4D3D-8728-54F26595E89D@sanger.ac.uk> Hi all Owing to problems with our data centre cooling system, the Sanger network will be offline from around 4.30pm on Friday 7th January until the evening of Sunday 9th January (UK time). This means that all UK-based Ensembl sites, including www.ensembl.org, archives and pre site, will be unavailable from late Friday afternoon until Monday morning. Our US mirror sites will be available, but services that depend on machines based in the UK, i.e. BLAST/BLAT and user logins, will be disabled during this time. Please accept our apologies for any inconvenience caused. A reminder will be sent out nearer the time. Regards Anne Anne Parker Ensembl Web Production Manager http://www.ensembl.org From st3 at sanger.ac.uk Wed Dec 22 14:30:17 2010 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Wed, 22 Dec 2010 14:30:17 +0000 Subject: [ensembl-announce] BLAST maintenance In-Reply-To: <4A267A65-89D3-4027-BCE9-902E01EFC218@sanger.ac.uk> References: <4A267A65-89D3-4027-BCE9-902E01EFC218@sanger.ac.uk> Message-ID: <4D120B79.10000@sanger.ac.uk> The maintenance has been completed and BLAST is now back online. Regards, Steve On 12/21/10 16:10, Anne Parker wrote: > Hi all > > The routine maintenance of our BLAST databases has been rescheduled > for tomorrow, Wednesday 22nd December, around 10am UK time. We will > let you know when work is complete; please accept our apologies for > any inconvenience caused. > > Regards > > Anne > > > Anne Parker > Ensembl Web Production Manager > http://www.ensembl.org > > > > > _______________________________________________ > Announce mailing list > Announce at ensembl.org > http://lists.ensembl.org/mailman/listinfo/announce