From st3 at sanger.ac.uk Mon Jan 7 12:17:44 2013 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Mon, 07 Jan 2013 12:17:44 +0000 Subject: [ensembl-announce] Ensembl FTP site downtime (Tue 8th Jan) Message-ID: <50EABCE8.5060905@sanger.ac.uk> Dear all, The Ensembl FTP site will be unavailable from 1100 GMT on Tue 8th Jan whilst we carry out some urgent hardware maintenance. We expect this to be completed within two hours. Apologies for the short notice and the inconvenience it may cause. No other Ensembl resources will be affected. Regards, Steve From flicek at ebi.ac.uk Tue Jan 15 17:35:35 2013 From: flicek at ebi.ac.uk (Paul Flicek) Date: Tue, 15 Jan 2013 17:35:35 +0000 Subject: [ensembl-announce] Potential update to Ensembl license Message-ID: <33E51DF9-7081-4E57-A9CD-B436EA809DE1@ebi.ac.uk> Dear Ensembl users and developers, Since our launch in 1999, the Ensembl software has been licensed under a lightly modified Apache version 1 license (http://www.ensembl.org/info/about/legal/code_licence.html). In 2004 Apache itself stopped using this license in f savour of the Apache version 2 license, which has since developed into one of the standard and most widely used permissive licenses in open source software. For those interested, details of Apache's licenses and their history is here http://www.apache.org/licenses/. At Ensembl we are considering updating the license for all of Ensembl code for which we have copyright to the Apache version 2 license. This change will have the benefit of being more explicit in the rights granted and by adopting a well known and highly used license, we also believe that this will be organisations wishing to use our code will better understand how our code is licensed. We believe there is wide comfort and experience using the Apache version 2 license within the community. Most importantly, we believe that this change would allow all of our users to do exactly the same things they are doing now and support them to build new and great things. This proposed license change will also apply to the eHive code parts of which are licensed "under the same terms as Perl itself." If you have any comments or questions about this change please contact me directly (i.e. please do not reply to the list) by 1 February 2013 if possible. I will post back a summary of questions and comments received (if any) along with any further news. This change to the Ensembl software license will not effect the status of the data within Ensembl, which is provided without any restriction by the project. Thank you for your continued support of Ensembl. Paul Flicek From rhoda at ebi.ac.uk Thu Jan 17 11:27:41 2013 From: rhoda at ebi.ac.uk (Rhoda Kinsella) Date: Thu, 17 Jan 2013 11:27:41 +0000 Subject: [ensembl-announce] Ensembl release 70 is out! Message-ID: <679A7186-F001-4C99-A29C-60AD6242A97C@ebi.ac.uk> We are pleased to announce that the latest Ensembl update (e!70) has been released : http://www.ensembl.org/ Highlights of this release include: Human: Updated patches for the Human assembly (GRCh37.p10) and reanalysed Human BodyMap data from Illumina using the recently updated RNASeq pipeline. Imported HGMD-PUBLIC sequence variation data from release 2012.3 with regulatory data for Human. Other species: A new regulatory build for Mouse including a much broader coverage for the Embryonic Fibroblast (MEF) build and additional data on other cell types. Inclusion of first GRC patches for the Mouse assembly (GRCm38.p1). New assemblies for Rat (Rnor 5.0) and Cat (Felis catus 6.2) and a new gene set for Fruitfly (FlyBase version 5.46). Other news: New web features for sharing pages and images and a streamlined interface for uploading user data. A complete list of the changes in release 70 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/2013/01/17/ensembl-70-has-been-released/ Best regards, Rhoda Kinsella Rhoda Kinsella Ph.D. Ensembl Production Project Leader, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD -------------- next part -------------- An HTML attachment was scrubbed... URL: From dstaines at ebi.ac.uk Mon Jan 28 17:05:57 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Mon, 28 Jan 2013 17:05:57 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 17 Intentions In-Reply-To: <50A110F7.5070205@ebi.ac.uk> References: <50A110F7.5070205@ebi.ac.uk> Message-ID: <5106AFF5.4040701@ebi.ac.uk> Please note that release 17 of Ensembl Genomes has been delayed and is now due for release on Feburary 7th. Apologies 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 st3 at sanger.ac.uk Mon Jan 7 12:17:44 2013 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Mon, 07 Jan 2013 12:17:44 +0000 Subject: [ensembl-announce] Ensembl FTP site downtime (Tue 8th Jan) Message-ID: <50EABCE8.5060905@sanger.ac.uk> Dear all, The Ensembl FTP site will be unavailable from 1100 GMT on Tue 8th Jan whilst we carry out some urgent hardware maintenance. We expect this to be completed within two hours. Apologies for the short notice and the inconvenience it may cause. No other Ensembl resources will be affected. Regards, Steve From flicek at ebi.ac.uk Tue Jan 15 17:35:35 2013 From: flicek at ebi.ac.uk (Paul Flicek) Date: Tue, 15 Jan 2013 17:35:35 +0000 Subject: [ensembl-announce] Potential update to Ensembl license Message-ID: <33E51DF9-7081-4E57-A9CD-B436EA809DE1@ebi.ac.uk> Dear Ensembl users and developers, Since our launch in 1999, the Ensembl software has been licensed under a lightly modified Apache version 1 license (http://www.ensembl.org/info/about/legal/code_licence.html). In 2004 Apache itself stopped using this license in f savour of the Apache version 2 license, which has since developed into one of the standard and most widely used permissive licenses in open source software. For those interested, details of Apache's licenses and their history is here http://www.apache.org/licenses/. At Ensembl we are considering updating the license for all of Ensembl code for which we have copyright to the Apache version 2 license. This change will have the benefit of being more explicit in the rights granted and by adopting a well known and highly used license, we also believe that this will be organisations wishing to use our code will better understand how our code is licensed. We believe there is wide comfort and experience using the Apache version 2 license within the community. Most importantly, we believe that this change would allow all of our users to do exactly the same things they are doing now and support them to build new and great things. This proposed license change will also apply to the eHive code parts of which are licensed "under the same terms as Perl itself." If you have any comments or questions about this change please contact me directly (i.e. please do not reply to the list) by 1 February 2013 if possible. I will post back a summary of questions and comments received (if any) along with any further news. This change to the Ensembl software license will not effect the status of the data within Ensembl, which is provided without any restriction by the project. Thank you for your continued support of Ensembl. Paul Flicek From rhoda at ebi.ac.uk Thu Jan 17 11:27:41 2013 From: rhoda at ebi.ac.uk (Rhoda Kinsella) Date: Thu, 17 Jan 2013 11:27:41 +0000 Subject: [ensembl-announce] Ensembl release 70 is out! Message-ID: <679A7186-F001-4C99-A29C-60AD6242A97C@ebi.ac.uk> We are pleased to announce that the latest Ensembl update (e!70) has been released : http://www.ensembl.org/ Highlights of this release include: Human: Updated patches for the Human assembly (GRCh37.p10) and reanalysed Human BodyMap data from Illumina using the recently updated RNASeq pipeline. Imported HGMD-PUBLIC sequence variation data from release 2012.3 with regulatory data for Human. Other species: A new regulatory build for Mouse including a much broader coverage for the Embryonic Fibroblast (MEF) build and additional data on other cell types. Inclusion of first GRC patches for the Mouse assembly (GRCm38.p1). New assemblies for Rat (Rnor 5.0) and Cat (Felis catus 6.2) and a new gene set for Fruitfly (FlyBase version 5.46). Other news: New web features for sharing pages and images and a streamlined interface for uploading user data. A complete list of the changes in release 70 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/2013/01/17/ensembl-70-has-been-released/ Best regards, Rhoda Kinsella Rhoda Kinsella Ph.D. Ensembl Production Project Leader, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD -------------- next part -------------- An HTML attachment was scrubbed... URL: From dstaines at ebi.ac.uk Mon Jan 28 17:05:57 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Mon, 28 Jan 2013 17:05:57 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 17 Intentions In-Reply-To: <50A110F7.5070205@ebi.ac.uk> References: <50A110F7.5070205@ebi.ac.uk> Message-ID: <5106AFF5.4040701@ebi.ac.uk> Please note that release 17 of Ensembl Genomes has been delayed and is now due for release on Feburary 7th. Apologies 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/