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Ensembl update 2010

Collection published: 30 October 2010

This thematic series of methods papers describes the construction, content and use of Ensembl's resources. Ensembl is a joint project of the European Bioinformatics Institute (a part of the European Molecular Biology Laboratory) and the Wellcome Trust Sanger Institute. Ensembl enables genomic science by providing high quality, integrated annotation on vertebrate genomes within a consistent and accessible infrastructure. Components of the Ensembl project include the genome browser at http://www.ensembl.org, the Ensembl gene sets, the Ensembl API software and other data resources.

		Correspondence Touring Ensembl: A practical guide to genome browsing Giulietta M Spudich, Xosé M Fernández-Suárez BMC Genomics 2010, 11:295 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Consistent annotation of gene expression arrays Benoît Ballester, Nathan Johnson, Glenn Proctor, Paul Flicek BMC Genomics 2010, 11:294 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Database Ensembl variation resources Yuan Chen, Fiona Cunningham, Daniel Rios, William M McLaren, James Smith, Bethan Pritchard, Giulietta M Spudich, Simon Brent, Eugene Kulesha, Pablo Marin-Garcia, Damian Smedley, Ewan Birney, Paul Flicek BMC Genomics 2010, 11:293 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Ensembl project collates variation in genome sequences across a large number of chordate species and the recent update describes the comprehensive web-based functions available for tabulating and visualizing genome variants.
		Methodology article eHive: An Artificial Intelligence workflow system for genomic analysis Jessica Severin, Kathryn Beal, Albert J Vilella, Stephen Fitzgerald, Michael Schuster, Leo Gordon, Abel Ureta-Vidal, Paul Flicek, Javier Herrero BMC Bioinformatics 2010, 11:240 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Due to the ever increasing number of genomes reported, ENSEMBL has implemented an artificial intelligence pipeline ‘ eHIVE’, based on a self-organizing workflow system, to provide updates to its comparative genomics resources.
		Correspondence Using caching and optimization techniques to improve performance of the Ensembl website Anne Parker, Eugene Bragin, Simon Brent, Bethan Pritchard, James A Smith, Stephen Trevanion BMC Bioinformatics 2010, 11:239 (11 May 2010) Abstract \| Full text \| PDF \| PubMed
		Software A database and API for variation, dense genotyping and resequencing data Daniel Rios, William M McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek, Fiona Cunningham BMC Bioinformatics 2010, 11:238 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central

		Correspondence Touring Ensembl: A practical guide to genome browsing Giulietta M Spudich, Xosé M Fernández-Suárez BMC Genomics 2010, 11:295 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Methodology article Consistent annotation of gene expression arrays Benoît Ballester, Nathan Johnson, Glenn Proctor, Paul Flicek BMC Genomics 2010, 11:294 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Database Ensembl variation resources Yuan Chen, Fiona Cunningham, Daniel Rios, William M McLaren, James Smith, Bethan Pritchard, Giulietta M Spudich, Simon Brent, Eugene Kulesha, Pablo Marin-Garcia, Damian Smedley, Ewan Birney, Paul Flicek BMC Genomics 2010, 11:293 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Ensembl project collates variation in genome sequences across a large number of chordate species and the recent update describes the comprehensive web-based functions available for tabulating and visualizing genome variants.
		Methodology article eHive: An Artificial Intelligence workflow system for genomic analysis Jessica Severin, Kathryn Beal, Albert J Vilella, Stephen Fitzgerald, Michael Schuster, Leo Gordon, Abel Ureta-Vidal, Paul Flicek, Javier Herrero BMC Bioinformatics 2010, 11:240 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Due to the ever increasing number of genomes reported, ENSEMBL has implemented an artificial intelligence pipeline ‘ eHIVE’, based on a self-organizing workflow system, to provide updates to its comparative genomics resources.
		Correspondence Using caching and optimization techniques to improve performance of the Ensembl website Anne Parker, Eugene Bragin, Simon Brent, Bethan Pritchard, James A Smith, Stephen Trevanion BMC Bioinformatics 2010, 11:239 (11 May 2010) Abstract \| Full text \| PDF \| PubMed
		Software A database and API for variation, dense genotyping and resequencing data Daniel Rios, William M McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek, Fiona Cunningham BMC Bioinformatics 2010, 11:238 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central