From maurel at ebi.ac.uk Wed Jul 3 15:11:27 2013 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Wed, 3 Jul 2013 15:11:27 +0100 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 73 Message-ID: Dear all, Please find the summary of the declarations of intentions for Ensembl release 73 (scheduled for the 28th of August 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 Jul 5 13:07:45 2013 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Fri, 5 Jul 2013 13:07:45 +0100 Subject: [ensembl-announce] Ensembl Genomes release 19: announcement Message-ID: <0D340741-275E-4D9D-8607-C53F2E9004EE@ebi.ac.uk> Dear all, Ensembl Genomes release 19 is out! The release contains new and updated genomes and associated data, which can be accessible via the Ensembl Genomes website, the REST web service, the Perl APIs and the FTP site. The detailed features of this new release are: Ensembl Metazoa * New genomes Rhodnius prolixus (a hemipteran, imported from VectorBase) Tetranychus urticae (two-spotted spider mite, a chelicerate) Crassostrea gigas (Pacific oyster) Lottia gigantea (owl limpet) Capitella teleta (polychaete worm) Helobdella robusta (leech) * New data Synteny, based on orthology, between Drosophila melanogaster and Anopheles gambiae * Updated data Peptide comparative genomics and BioMart Ensembl Fungi * Updated genomes S. pombe (PomBase v36) * New data Transcript profiling RNA-Seq for Zymoseptoria tritici (SRA study SRP017084) * Updated data Annotations of pathogenic phenotype imported from PHI-base Ensembl Protists * New genomes Paramecium tetraurelia (Ciliate) * Updated data Peptide compara and Biomart Ensembl Plants * New genomes Triticum urartu (wheat A-genome progenitor) Aegilops tauschii (wheat D-genome progenitor) New data Bread wheat genome alignments to barley * Updated data Barley variations and BioMart Ensembl Bacteria * No significant updates Let us know what you think of our new release on helpdesk at ensemblgenomes.org note: the public MySQL and FTP will be available shortly. The Ensembl Genomes Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From dstaines at ebi.ac.uk Fri Jul 5 14:49:45 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Fri, 05 Jul 2013 14:49:45 +0100 Subject: [ensembl-announce] Restart of Ensembl Genomes public MySQL instances Message-ID: <51D6CEF9.2030908@ebi.ac.uk> We are currently experiencing problems with the public MySQL instance for Ensembl Genomes (mysql.ebi.ac.uk:4157) and need to carry out an urgent restart to resolve some issues. This will happen at 3.30pm today, and is likely to last a few minutes. Apologies for the short notice. Dan Staines. -- 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 Mon Jul 8 07:32:58 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Mon, 08 Jul 2013 07:32:58 +0100 Subject: [ensembl-announce] Ensembl Genomes MySQL server outage Message-ID: The public Ensembl Genomes MySQL server, mysql.ebi.ac.uk:4157 is server is currently unavailable, and we are working to address this. Please accept our apologies for inconvenience caused by the outage - we will announce when service has been restored. Regards, Dan Staines. -- 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 Mon Jul 8 14:25:26 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Mon, 08 Jul 2013 14:25:26 +0100 Subject: [ensembl-announce] Ensembl Genomes MySQL server outage In-Reply-To: <4B2DE8422AF25D40820C088EF2AE5D272FD86E5445@EXSEEDMD.is.ed.ac.uk> References: <4B2DE8422AF25D40820C088EF2AE5D272FD86E5445@EXSEEDMD.is.ed.ac.uk> Message-ID: <51DABDC6.5050204@ebi.ac.uk> On 07/08/2013 02:17 PM, PATERSON Trevor wrote: > I know you are having problems with the public genomes mysql database at the moment.. > > Do you have a time table for when you will be rolling out the _core_19_72 databases? Nothing concrete at the moment, I'm afraid. I hope it will be in the next few days but depends on resolving some blocking issues with the public server. 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 dstaines at ebi.ac.uk Tue Jul 9 14:02:41 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 09 Jul 2013 14:02:41 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 20 Intentions Message-ID: <51DC09F1.6080205@ebi.ac.uk> Dear all, Release 20 of Ensembl Genomes is scheduled for 10th September 2013 - our intentions for this release can be found here: http://ensemblgenomes.org/info/release/EG20 Please note these are intentions and are therefore not guaranteed to be completed for September. 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 Jul 11 10:46:39 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 11 Jul 2013 10:46:39 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 19 Database & FTP Availability Message-ID: <51DE7EFF.1040909@ebi.ac.uk> We are pleased to inform you that release 19 of Ensembl Genomes is now available from our FTP site: ftp://ftp.ensemblgenomes.org/pub/release-19 Release 19 databases are also available from our public MySQL server (anonymous at mysql.ebi.ac.uk:4157). Please note that the final few tables of plants_snp_mart_19 and plants_mart_19 are still loading, and should be finished later today. Please accept our apologies for the delay in releasing this data. We are planning an upgrade to our public MySQL hardware to avoid delays of this kind in future. Regards, Dan Staines. -- 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 st3 at sanger.ac.uk Thu Jul 25 17:20:16 2013 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Thu, 25 Jul 2013 17:20:16 +0100 Subject: [ensembl-announce] Ensembl website downtime Fri 26th July Message-ID: <51F15040.5070306@sanger.ac.uk> Dear all, The Hinxton based Ensembl website (www.ensembl.org) and archives 62-71 will be offline for a short period on Friday morning for urgent hardware maintenance. This will start at 0900 GMT and should be finished within the hour. Mirror sites will be unaffected apart from losing BLAST and BLAT services. Apologies for the short notice and any inconvenience caused. Regards, Steve From maurel at ebi.ac.uk Wed Jul 3 15:11:27 2013 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Wed, 3 Jul 2013 15:11:27 +0100 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 73 Message-ID: Dear all, Please find the summary of the declarations of intentions for Ensembl release 73 (scheduled for the 28th of August 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 Jul 5 13:07:45 2013 From: denise at ebi.ac.uk (Denise Carvalho-Silva) Date: Fri, 5 Jul 2013 13:07:45 +0100 Subject: [ensembl-announce] Ensembl Genomes release 19: announcement Message-ID: <0D340741-275E-4D9D-8607-C53F2E9004EE@ebi.ac.uk> Dear all, Ensembl Genomes release 19 is out! The release contains new and updated genomes and associated data, which can be accessible via the Ensembl Genomes website, the REST web service, the Perl APIs and the FTP site. The detailed features of this new release are: Ensembl Metazoa * New genomes Rhodnius prolixus (a hemipteran, imported from VectorBase) Tetranychus urticae (two-spotted spider mite, a chelicerate) Crassostrea gigas (Pacific oyster) Lottia gigantea (owl limpet) Capitella teleta (polychaete worm) Helobdella robusta (leech) * New data Synteny, based on orthology, between Drosophila melanogaster and Anopheles gambiae * Updated data Peptide comparative genomics and BioMart Ensembl Fungi * Updated genomes S. pombe (PomBase v36) * New data Transcript profiling RNA-Seq for Zymoseptoria tritici (SRA study SRP017084) * Updated data Annotations of pathogenic phenotype imported from PHI-base Ensembl Protists * New genomes Paramecium tetraurelia (Ciliate) * Updated data Peptide compara and Biomart Ensembl Plants * New genomes Triticum urartu (wheat A-genome progenitor) Aegilops tauschii (wheat D-genome progenitor) New data Bread wheat genome alignments to barley * Updated data Barley variations and BioMart Ensembl Bacteria * No significant updates Let us know what you think of our new release on helpdesk at ensemblgenomes.org note: the public MySQL and FTP will be available shortly. The Ensembl Genomes Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From dstaines at ebi.ac.uk Fri Jul 5 14:49:45 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Fri, 05 Jul 2013 14:49:45 +0100 Subject: [ensembl-announce] Restart of Ensembl Genomes public MySQL instances Message-ID: <51D6CEF9.2030908@ebi.ac.uk> We are currently experiencing problems with the public MySQL instance for Ensembl Genomes (mysql.ebi.ac.uk:4157) and need to carry out an urgent restart to resolve some issues. This will happen at 3.30pm today, and is likely to last a few minutes. Apologies for the short notice. Dan Staines. -- 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 Mon Jul 8 07:32:58 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Mon, 08 Jul 2013 07:32:58 +0100 Subject: [ensembl-announce] Ensembl Genomes MySQL server outage Message-ID: The public Ensembl Genomes MySQL server, mysql.ebi.ac.uk:4157 is server is currently unavailable, and we are working to address this. Please accept our apologies for inconvenience caused by the outage - we will announce when service has been restored. Regards, Dan Staines. -- 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 Mon Jul 8 14:25:26 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Mon, 08 Jul 2013 14:25:26 +0100 Subject: [ensembl-announce] Ensembl Genomes MySQL server outage In-Reply-To: <4B2DE8422AF25D40820C088EF2AE5D272FD86E5445@EXSEEDMD.is.ed.ac.uk> References: <4B2DE8422AF25D40820C088EF2AE5D272FD86E5445@EXSEEDMD.is.ed.ac.uk> Message-ID: <51DABDC6.5050204@ebi.ac.uk> On 07/08/2013 02:17 PM, PATERSON Trevor wrote: > I know you are having problems with the public genomes mysql database at the moment.. > > Do you have a time table for when you will be rolling out the _core_19_72 databases? Nothing concrete at the moment, I'm afraid. I hope it will be in the next few days but depends on resolving some blocking issues with the public server. 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 dstaines at ebi.ac.uk Tue Jul 9 14:02:41 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 09 Jul 2013 14:02:41 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 20 Intentions Message-ID: <51DC09F1.6080205@ebi.ac.uk> Dear all, Release 20 of Ensembl Genomes is scheduled for 10th September 2013 - our intentions for this release can be found here: http://ensemblgenomes.org/info/release/EG20 Please note these are intentions and are therefore not guaranteed to be completed for September. 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 Jul 11 10:46:39 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 11 Jul 2013 10:46:39 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 19 Database & FTP Availability Message-ID: <51DE7EFF.1040909@ebi.ac.uk> We are pleased to inform you that release 19 of Ensembl Genomes is now available from our FTP site: ftp://ftp.ensemblgenomes.org/pub/release-19 Release 19 databases are also available from our public MySQL server (anonymous at mysql.ebi.ac.uk:4157). Please note that the final few tables of plants_snp_mart_19 and plants_mart_19 are still loading, and should be finished later today. Please accept our apologies for the delay in releasing this data. We are planning an upgrade to our public MySQL hardware to avoid delays of this kind in future. Regards, Dan Staines. -- 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 st3 at sanger.ac.uk Thu Jul 25 17:20:16 2013 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Thu, 25 Jul 2013 17:20:16 +0100 Subject: [ensembl-announce] Ensembl website downtime Fri 26th July Message-ID: <51F15040.5070306@sanger.ac.uk> Dear all, The Hinxton based Ensembl website (www.ensembl.org) and archives 62-71 will be offline for a short period on Friday morning for urgent hardware maintenance. This will start at 0900 GMT and should be finished within the hour. Mirror sites will be unaffected apart from losing BLAST and BLAT services. Apologies for the short notice and any inconvenience caused. Regards, Steve