From dstaines at ebi.ac.uk Thu Oct 13 16:58:38 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 13 Oct 2011 16:58:38 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 12 intentions Message-ID: <4E970AAE.1090206@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 12 of Ensembl Genomes, due out on 13th December 2011. Please note these are intentions and are therefore not guaranteed to be completed for December. These can also be viewed online at: http://ensemblgenomes.org/info/release12 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. General - release scheduled for 13th December 2011 - update to Ensembl 65 software - new Pan Compara database - updated pan concern databases from Ensembl Metazoa - addition of Atta cephalotes genome - addition of Bombyx mori genome - addition of Tribolium casteneum genome - updated compara - updated biomart Bacteria - update to Escherichia/Shigella clade database to show operon data from RegulonDB for E. coli K12 - updated peptide compara database - updated biomarts Protists - addition of Cyanidioschyzon merolae 10D genome - updated peptide compara database - updated biomarts Fungi - update of Schizosaccharomyces pombe to latest PomBase data addition of Ashbya gossypii genome - removal of 2-micron plasmid from the Saccharomyces cerevisiae reference genome - updated Gibberella zeae variations with rsIDs - updated crossreferences for Mycosphaerella graminicola - addition of DNA alignments between Ashbya gossypii and Saccharomyces cerevisiae - updated peptide compara database - updated biomarts Plants - update to soybean gene set - updated sorghum protein features/cross-references - updated peptide compara - updated 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 ap5 at sanger.ac.uk Fri Oct 14 14:35:10 2011 From: ap5 at sanger.ac.uk (Anne Parker) Date: Fri, 14 Oct 2011 14:35:10 +0100 Subject: [ensembl-announce] Ensembl downtime Message-ID: <494B9EDF-39D5-4FE3-B5AF-010A2942395E@sanger.ac.uk> The Sanger datacentre will be closing down for maintenance from midday (UK time) on Friday 21st October, until the evening of Sunday 23rd October. As a result all Sanger-hosted Ensembl websites, including www.ensembl.org, Vega, Pre!, beta and archives, will be offline for this period. Mirror sites should remain online, but services dependent on Sanger systems, including user accounts and BLAST, will not be available. Please accept our apologies for any inconvenience caused. Regards Anne Parker Ensembl Web Production Manager http://www.ensembl.org From gspudich at ebi.ac.uk Tue Oct 18 16:59:35 2011 From: gspudich at ebi.ac.uk (Giulietta) Date: Tue, 18 Oct 2011 16:59:35 +0100 Subject: [ensembl-announce] Reminder: Workshop on Gene Annotation 1-2 Nov Message-ID: <4E9DA267.3090501@ebi.ac.uk> Hello all, The Ensembl Gene Annotation workshop at CSHL is coming up! Although this workshop is free of charge, you have to register by sending an email to bert at ebi.ac.uk in order to attend. Please register so we know the numbers. If there is not enough interest, we won't hold the workshop, so please pass this on to any interested colleagues who will be around CSHL at the beginning of November. Two genebuilders from Ensembl will lead the workshop, and it is an excellent chance to understand and explore the Ensembl annotation pipeline. Regards, Giulietta (Ensembl Outreach) Workshop details: Ensembl is holding a workshop titled, "Introduction to automatic gene annotation". This workshop, running 1-2 November at CSHL, is aimed at developers. Two Ensembl developers will present sessions on how to create your own core database, including the loading of a genome assembly into a database and the running of simple analyses using the Ensembl genebuild pipeline. This meeting will therefore follow the same format as the 2007-2010 automatic gene annotation workshops. Participants will be expected to have experience in programming and a background in object-oriented programming. A good familiarity with Perl, a Unix/Linux environment, and MySQL are essential to follow the workshop and the programming examples. Knowledge of the Ensembl core API is also essential. We will be working from a Virtual Machine and participants are expected to bring their own laptops (preferably Mac) to work from -- more details will be provided on registration. Topics to be presented: * Introduction to the GeneBuild pipeline, including data input types, generating protein-coding transcript models, and adding UTR to these models * An introduction to assembly structure (toplevel, contigs, scaffolds, chromosomes) * Overview of the different Ensembl APIs * Obtaining the Ensembl API (cvs checkout) * Core database schema * Tracking jobs in the pipeline * Runnable and RunnableDB modules Practical sessions: * Creating a genebuild database * Loading an assembly into the database * Running algorithms first on the commandline and then using the pipeline * Understanding how the pipeline code interacts with the algorithms and the database * Understanding the pipeline's job tracking system * Visualisation of results with Apollo. Registration for this workshop is free, but participants will need to cover their own accommodation and meal expenses. Would you like to join us? Please contact Bert (bert at ebi.ac.uk ) for more details or to register. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dstaines at ebi.ac.uk Wed Oct 19 08:07:12 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Wed, 19 Oct 2011 08:07:12 +0100 Subject: [ensembl-announce] downtime of Ensembl Plants biomart Message-ID: <4E9E7720.7010704@ebi.ac.uk> The Ensembl Plants biomart server needs to be taken down for essential maintenance today. The server will be taken down at 10am BST and we anticipate downtime of several hours. A further announcement will be made once the server is available again. Apologies for any inconvenience this may cause and the short notice required. -- 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 Wed Oct 19 21:42:25 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Wed, 19 Oct 2011 21:42:25 +0100 Subject: [ensembl-announce] downtime of Ensembl Plants biomart In-Reply-To: <4E9E76F5.2060401@ebi.ac.uk> References: <4E9E76F5.2060401@ebi.ac.uk> Message-ID: <4E9F3631.3000306@ebi.ac.uk> The Ensembl Plants biomart is now available again. Please let us know if you encounter any problems. Regards, Dan Staines. From ap5 at sanger.ac.uk Thu Oct 20 11:50:41 2011 From: ap5 at sanger.ac.uk (Anne Parker) Date: Thu, 20 Oct 2011 11:50:41 +0100 Subject: [ensembl-announce] Ensembl websites offline for maintenance Message-ID: Dear all We would like to remind you that all Sanger-based Ensembl websites and related services will go offline around midday tomorrow, Friday 21st October. This will affect the main Ensembl website, archives, Pre! and beta. Mirror sites (US and Asia) will remain available, but Sanger-dependent services, including BLAST and user accounts, will be disabled. We hope that the datacentre restart will go smoothly and the sites will be back online by Monday morning at the latest - if you find a site is not working as expected by noon UK time, please let us know so that we can investigate. 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 Thu Oct 20 14:31:18 2011 From: ap5 at sanger.ac.uk (Anne Parker) Date: Thu, 20 Oct 2011 14:31:18 +0100 Subject: [ensembl-announce] Sanger downtime - addendum Message-ID: <6198497F-5946-4D73-8BA7-2B04442D2985@sanger.ac.uk> Hi all An astute user has asked if the Ensembl public MySQL instances will be offline this week, along with the websites. The answer, sadly, is yes. The entire Sanger datacentre is being switched off - only a skeleton frontend will be run, to display notification pages and ensure that our web domains don't disappear from the 'net completely! Regards Anne Anne Parker Ensembl Web Production Manager http://www.ensembl.org From ap5 at sanger.ac.uk Thu Oct 20 14:38:54 2011 From: ap5 at sanger.ac.uk (Anne Parker) Date: Thu, 20 Oct 2011 14:38:54 +0100 Subject: [ensembl-announce] Public mirror databases Message-ID: <745A4363-68F2-4B62-9553-FA0F8F97EDF5@sanger.ac.uk> I have just been reminded that we do have a mirror copy of the current release's databases _only_ (i.e. release 64 only, no archives): useastdb.ensembl.org:5306 This will remain available over the shutdown period. Cheers Anne Anne Parker Ensembl Web Production Manager http://www.ensembl.org From dstaines at ebi.ac.uk Thu Oct 20 15:38:12 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 20 Oct 2011 15:38:12 +0100 Subject: [ensembl-announce] Downtime of Ensembl Genomes public MySQL server Message-ID: <4EA03254.2050002@ebi.ac.uk> As part of a planned temporary data centre shutdown in Hinxton, the Ensembl Genomes public MySQL server (mysql.ebi.ac.uk:4157) will be unavailable between Friday 21 October 2011 at 14.00 (GMT+1) and Monday 24 October at 12.00 (GMT+1). The Ensembl Genomes web portals will remain available during this time. We apologise for any incovenience this may cause. Regards, Dan Staines, on behalf of the Ensembl Genomes team. From bert at ebi.ac.uk Mon Oct 24 10:59:08 2011 From: bert at ebi.ac.uk (bert at ebi.ac.uk) Date: Mon, 24 Oct 2011 10:59:08 +0100 (BST) Subject: [ensembl-announce] Ensembl API workshop 30 Nov - 2 Dec 2011 Cambridge UK Message-ID: <38055.172.22.68.204.1319450348.squirrel@webmail.ebi.ac.uk> Hello all, >From Wednesday November 30th till Friday December 2nd 2011 the Ensembl team will give another Ensembl API workshop at the Genetics Department of the University of Cambridge in the UK. Description: The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 3-day workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers the core, compara, variation and functional genomics (regulation) databases and APIs. For each of these the database schema and the API design as well as its most important objects and their methods will be presented. This will be followed by practical sessions in which the participants can put the learned into practice by writing their own Perl scripts. There are no costs for the workshop. Requirements: IMPORTANT: This workshop is NOT intended to teach you either Perl or molecular biological and genetic concepts! To be able to attend you should be able to code in Perl and be familiar with basic molecular biology and genetics. A basic knowledge of Ensembl is advantageous. Schedule: The schedule for the workshop will be as follows: Wednesday 30 November: 09:30 - 14:30: Core API 14:30 - 17:00: Functional Genomics API Thursday 1 December: 09:30 - 11:30: Functional Genomics API 11:30 - 17:00: Variation API Friday 2 December: 09:30 - 17:00: Compara API Registration: To register for this workshop, please go to: http://training.csx.cam.ac.uk/programme/261407 At the moment I write this mail the workshop still hasn't been advertised on above mentioned site. As long as this is the case, please register by contacting David Judge (dpj10 at cam.ac.uk) directly. More information: If you have any questions about the workshop you can mail me at bert at ebi.ac.uk. Cheers, Bert -- Bert Overduin, Ph.D. Vertebrate Genomics Team EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom http://www.ebi.ac.uk/~bert Ensembl browser: http://www.ensembl.org Mailing lists: http://www.ensembl.org/info/about/contact/mailing.html Blog: http://www.ensembl.info YouTube: http://www.youtube.com/user/EnsemblHelpdesk Facebook: http://www.facebook.com/Ensembl.org Twitter: http://twitter.com/Ensembl From dstaines at ebi.ac.uk Thu Oct 13 16:58:38 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 13 Oct 2011 16:58:38 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 12 intentions Message-ID: <4E970AAE.1090206@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 12 of Ensembl Genomes, due out on 13th December 2011. Please note these are intentions and are therefore not guaranteed to be completed for December. These can also be viewed online at: http://ensemblgenomes.org/info/release12 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. General - release scheduled for 13th December 2011 - update to Ensembl 65 software - new Pan Compara database - updated pan concern databases from Ensembl Metazoa - addition of Atta cephalotes genome - addition of Bombyx mori genome - addition of Tribolium casteneum genome - updated compara - updated biomart Bacteria - update to Escherichia/Shigella clade database to show operon data from RegulonDB for E. coli K12 - updated peptide compara database - updated biomarts Protists - addition of Cyanidioschyzon merolae 10D genome - updated peptide compara database - updated biomarts Fungi - update of Schizosaccharomyces pombe to latest PomBase data addition of Ashbya gossypii genome - removal of 2-micron plasmid from the Saccharomyces cerevisiae reference genome - updated Gibberella zeae variations with rsIDs - updated crossreferences for Mycosphaerella graminicola - addition of DNA alignments between Ashbya gossypii and Saccharomyces cerevisiae - updated peptide compara database - updated biomarts Plants - update to soybean gene set - updated sorghum protein features/cross-references - updated peptide compara - updated 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 ap5 at sanger.ac.uk Fri Oct 14 14:35:10 2011 From: ap5 at sanger.ac.uk (Anne Parker) Date: Fri, 14 Oct 2011 14:35:10 +0100 Subject: [ensembl-announce] Ensembl downtime Message-ID: <494B9EDF-39D5-4FE3-B5AF-010A2942395E@sanger.ac.uk> The Sanger datacentre will be closing down for maintenance from midday (UK time) on Friday 21st October, until the evening of Sunday 23rd October. As a result all Sanger-hosted Ensembl websites, including www.ensembl.org, Vega, Pre!, beta and archives, will be offline for this period. Mirror sites should remain online, but services dependent on Sanger systems, including user accounts and BLAST, will not be available. Please accept our apologies for any inconvenience caused. Regards Anne Parker Ensembl Web Production Manager http://www.ensembl.org From gspudich at ebi.ac.uk Tue Oct 18 16:59:35 2011 From: gspudich at ebi.ac.uk (Giulietta) Date: Tue, 18 Oct 2011 16:59:35 +0100 Subject: [ensembl-announce] Reminder: Workshop on Gene Annotation 1-2 Nov Message-ID: <4E9DA267.3090501@ebi.ac.uk> Hello all, The Ensembl Gene Annotation workshop at CSHL is coming up! Although this workshop is free of charge, you have to register by sending an email to bert at ebi.ac.uk in order to attend. Please register so we know the numbers. If there is not enough interest, we won't hold the workshop, so please pass this on to any interested colleagues who will be around CSHL at the beginning of November. Two genebuilders from Ensembl will lead the workshop, and it is an excellent chance to understand and explore the Ensembl annotation pipeline. Regards, Giulietta (Ensembl Outreach) Workshop details: Ensembl is holding a workshop titled, "Introduction to automatic gene annotation". This workshop, running 1-2 November at CSHL, is aimed at developers. Two Ensembl developers will present sessions on how to create your own core database, including the loading of a genome assembly into a database and the running of simple analyses using the Ensembl genebuild pipeline. This meeting will therefore follow the same format as the 2007-2010 automatic gene annotation workshops. Participants will be expected to have experience in programming and a background in object-oriented programming. A good familiarity with Perl, a Unix/Linux environment, and MySQL are essential to follow the workshop and the programming examples. Knowledge of the Ensembl core API is also essential. We will be working from a Virtual Machine and participants are expected to bring their own laptops (preferably Mac) to work from -- more details will be provided on registration. Topics to be presented: * Introduction to the GeneBuild pipeline, including data input types, generating protein-coding transcript models, and adding UTR to these models * An introduction to assembly structure (toplevel, contigs, scaffolds, chromosomes) * Overview of the different Ensembl APIs * Obtaining the Ensembl API (cvs checkout) * Core database schema * Tracking jobs in the pipeline * Runnable and RunnableDB modules Practical sessions: * Creating a genebuild database * Loading an assembly into the database * Running algorithms first on the commandline and then using the pipeline * Understanding how the pipeline code interacts with the algorithms and the database * Understanding the pipeline's job tracking system * Visualisation of results with Apollo. Registration for this workshop is free, but participants will need to cover their own accommodation and meal expenses. Would you like to join us? Please contact Bert (bert at ebi.ac.uk ) for more details or to register. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dstaines at ebi.ac.uk Wed Oct 19 08:07:12 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Wed, 19 Oct 2011 08:07:12 +0100 Subject: [ensembl-announce] downtime of Ensembl Plants biomart Message-ID: <4E9E7720.7010704@ebi.ac.uk> The Ensembl Plants biomart server needs to be taken down for essential maintenance today. The server will be taken down at 10am BST and we anticipate downtime of several hours. A further announcement will be made once the server is available again. Apologies for any inconvenience this may cause and the short notice required. -- 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 Wed Oct 19 21:42:25 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Wed, 19 Oct 2011 21:42:25 +0100 Subject: [ensembl-announce] downtime of Ensembl Plants biomart In-Reply-To: <4E9E76F5.2060401@ebi.ac.uk> References: <4E9E76F5.2060401@ebi.ac.uk> Message-ID: <4E9F3631.3000306@ebi.ac.uk> The Ensembl Plants biomart is now available again. Please let us know if you encounter any problems. Regards, Dan Staines. From ap5 at sanger.ac.uk Thu Oct 20 11:50:41 2011 From: ap5 at sanger.ac.uk (Anne Parker) Date: Thu, 20 Oct 2011 11:50:41 +0100 Subject: [ensembl-announce] Ensembl websites offline for maintenance Message-ID: Dear all We would like to remind you that all Sanger-based Ensembl websites and related services will go offline around midday tomorrow, Friday 21st October. This will affect the main Ensembl website, archives, Pre! and beta. Mirror sites (US and Asia) will remain available, but Sanger-dependent services, including BLAST and user accounts, will be disabled. We hope that the datacentre restart will go smoothly and the sites will be back online by Monday morning at the latest - if you find a site is not working as expected by noon UK time, please let us know so that we can investigate. 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 Thu Oct 20 14:31:18 2011 From: ap5 at sanger.ac.uk (Anne Parker) Date: Thu, 20 Oct 2011 14:31:18 +0100 Subject: [ensembl-announce] Sanger downtime - addendum Message-ID: <6198497F-5946-4D73-8BA7-2B04442D2985@sanger.ac.uk> Hi all An astute user has asked if the Ensembl public MySQL instances will be offline this week, along with the websites. The answer, sadly, is yes. The entire Sanger datacentre is being switched off - only a skeleton frontend will be run, to display notification pages and ensure that our web domains don't disappear from the 'net completely! Regards Anne Anne Parker Ensembl Web Production Manager http://www.ensembl.org From ap5 at sanger.ac.uk Thu Oct 20 14:38:54 2011 From: ap5 at sanger.ac.uk (Anne Parker) Date: Thu, 20 Oct 2011 14:38:54 +0100 Subject: [ensembl-announce] Public mirror databases Message-ID: <745A4363-68F2-4B62-9553-FA0F8F97EDF5@sanger.ac.uk> I have just been reminded that we do have a mirror copy of the current release's databases _only_ (i.e. release 64 only, no archives): useastdb.ensembl.org:5306 This will remain available over the shutdown period. Cheers Anne Anne Parker Ensembl Web Production Manager http://www.ensembl.org From dstaines at ebi.ac.uk Thu Oct 20 15:38:12 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 20 Oct 2011 15:38:12 +0100 Subject: [ensembl-announce] Downtime of Ensembl Genomes public MySQL server Message-ID: <4EA03254.2050002@ebi.ac.uk> As part of a planned temporary data centre shutdown in Hinxton, the Ensembl Genomes public MySQL server (mysql.ebi.ac.uk:4157) will be unavailable between Friday 21 October 2011 at 14.00 (GMT+1) and Monday 24 October at 12.00 (GMT+1). The Ensembl Genomes web portals will remain available during this time. We apologise for any incovenience this may cause. Regards, Dan Staines, on behalf of the Ensembl Genomes team. From bert at ebi.ac.uk Mon Oct 24 10:59:08 2011 From: bert at ebi.ac.uk (bert at ebi.ac.uk) Date: Mon, 24 Oct 2011 10:59:08 +0100 (BST) Subject: [ensembl-announce] Ensembl API workshop 30 Nov - 2 Dec 2011 Cambridge UK Message-ID: <38055.172.22.68.204.1319450348.squirrel@webmail.ebi.ac.uk> Hello all, >From Wednesday November 30th till Friday December 2nd 2011 the Ensembl team will give another Ensembl API workshop at the Genetics Department of the University of Cambridge in the UK. Description: The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 3-day workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers the core, compara, variation and functional genomics (regulation) databases and APIs. For each of these the database schema and the API design as well as its most important objects and their methods will be presented. This will be followed by practical sessions in which the participants can put the learned into practice by writing their own Perl scripts. There are no costs for the workshop. Requirements: IMPORTANT: This workshop is NOT intended to teach you either Perl or molecular biological and genetic concepts! To be able to attend you should be able to code in Perl and be familiar with basic molecular biology and genetics. A basic knowledge of Ensembl is advantageous. Schedule: The schedule for the workshop will be as follows: Wednesday 30 November: 09:30 - 14:30: Core API 14:30 - 17:00: Functional Genomics API Thursday 1 December: 09:30 - 11:30: Functional Genomics API 11:30 - 17:00: Variation API Friday 2 December: 09:30 - 17:00: Compara API Registration: To register for this workshop, please go to: http://training.csx.cam.ac.uk/programme/261407 At the moment I write this mail the workshop still hasn't been advertised on above mentioned site. As long as this is the case, please register by contacting David Judge (dpj10 at cam.ac.uk) directly. More information: If you have any questions about the workshop you can mail me at bert at ebi.ac.uk. Cheers, Bert -- Bert Overduin, Ph.D. Vertebrate Genomics Team EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom http://www.ebi.ac.uk/~bert Ensembl browser: http://www.ensembl.org Mailing lists: http://www.ensembl.org/info/about/contact/mailing.html Blog: http://www.ensembl.info YouTube: http://www.youtube.com/user/EnsemblHelpdesk Facebook: http://www.facebook.com/Ensembl.org Twitter: http://twitter.com/Ensembl