EMBL-EBI Now and in the Future

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• • • 3 07/03/2014 • • 07/03/2014 Time Item Speaker 09.45 Registration and refreshments 10.30 Programme Overview Dominic Clark (EMBL-EBI) 10.35 Welcome from EMBL-EBI Dame Janet Thornton, Director (EMBL-EBI). 10.55 Welcome from OneNucleus Tony Jones, Business Development Manager, (One Nucleus) 11.15 ELIXIR, the pan-European Niklas Blomberg, ELIXIR Director research infrastructure for biological information. 11.35 Overview of EMBL-EBI’s data Sarah Morgan (EMBL-EBI) resources and services 11.40 Genomics: 'Ensembl Giulietta Spudich, Ensembl Outreach Highlights: Accessing the Officer (EMBL-EBI) Genome' 12.10 Lunch and Networking 07/03/2014 13.30 Functional genomics: Array Robert Petryszak, Expression Atlas Express and the Expression Atlas Coordinator (EMBL-EBI) 13.55 Proteins: UniProt and proteomics Sandra Orchard, Proteomics Services services (including Reactome) Team Coordinator (EMBL-EBI) 14.20 Cheminformatics and metabolism Janna Hastings Group Coordinator, resources (including ChEBI) Cheminformatics and metabolism (EMBL- EBI) 14.40 Chemogenomics and bioactivity Anne Hersey, ChEMBL Coordinator resources (ChEMBL) (EMBL-EBI) 15.05 Overview of EMBL-EBI’s Web Rodrigo Lopez, Head of Web Production Services with worked examples (EMBL-EBI) 15.25 EMBL-EBI's training programme: Cath Brooksbank, Head of Training, improving accessibility to industrial EMBL-EBI users 15.45 ~ Coffee break ~ 07/03/2014 Applications and case studies 16.30 1000 Genomes project Chris Tyler-Smith, Wellcome Trust Sanger Institute 17.00 Pfizer/Neusentis case studies Alex Gutteridge, Pfizer Neusentis 17.45 Wrap-up discussion Dominic Clark (EMBL-EBI) and Aline Charpentier (One Nucleus) 18.00 Networking reception EMBL-EBI South Building 07/03/2014 Time Item 09.00 Welcome coffee 09.15 Dr. Gabriella Rustici: Functional genomics: Array Express and the Expression Atlas 10.45 Coffee 11.15 Dr. Sandra Orchard: Proteins: UniProt and proteomics services (including Reactome) 12.45 Close of training 07/03/2014 .

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Ensembl Genomes: Extending Ensembl Across the Taxonomic Space P
Published online 1 November 2009 Nucleic Acids Research, 2010, Vol. 38, Database issue D563–D569 doi:10.1093/nar/gkp871 Ensembl Genomes: Extending Ensembl across the taxonomic space P. J. Kersey*, D. Lawson, E. Birney, P. S. Derwent, M. Haimel, J. Herrero, S. Keenan, A. Kerhornou, G. Koscielny, A. Ka¨ ha¨ ri, R. J. Kinsella, E. Kulesha, U. Maheswari, K. Megy, M. Nuhn, G. Proctor, D. Staines, F. Valentin, A. J. Vilella and A. Yates EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK Received August 14, 2009; Revised September 28, 2009; Accepted September 29, 2009 ABSTRACT nucleotide archives; numerous other genomes exist in states of partial assembly and annotation; thousands of Ensembl Genomes (http://www.ensemblgenomes viral genomes sequences have also been generated. .org) is a new portal offering integrated access to Moreover, the increasing use of high-throughput genome-scale data from non-vertebrate species sequencing technologies is rapidly reducing the cost of of scientific interest, developed using the Ensembl genome sequencing, leading to an accelerating rate of genome annotation and visualisation platform. data production. This not only makes it likely that in Ensembl Genomes consists of five sub-portals (for the near future, the genomes of all species of scientiﬁc bacteria, protists, fungi, plants and invertebrate interest will be sequenced; but also the genomes of many metazoa) designed to complement the availability individuals, with the possibility of providing accurate and of vertebrate genomes in Ensembl. Many of the sophisticated annotation through the similarly low-cost databases supporting the portal have been built in application of functional assays.
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