The Ensembl Outreach team is currently looking into the possibility of giving some 1-day Ensembl browser workshops in the Western US in the period directly after the Plant and Animal Genome Conference in San Diego, which takes place from 9-13 January 2010. Hosting institutions would only have to pay the instructor’s expenses (accommodation and subsistence) and would share the domestic travel costs, but we would not otherwise charge for the workshops.
For more information about our browser workshops, please have a look here.
Interested? Please contact me for more details at bert@ebi.ac.uk.
Author: Bert Overduin
Go, go, go …. the new Ensembl ontology database and API
Starting with release 55 of Ensembl we provide an ensembl_ontology database. It replaces the older ensembl_go database which used to be loaded straight from the public table dumps provided by the Gene Ontology group (and hence wasn’t really an Ensembl database to start with). The associated API is now part of the Ensembl Core API, which should make working with GO terms in Ensembl more straightforward than it was in the past. Available methods include, amongst others, fetching all parent or child terms of a given GO term and fetching all genes, transcripts or translations annotated with a given GO term.
More detailed documentation on both database and API can be found at ensembl/misc-scripts/ontology/README.
Credit for developing the ensembl_ontology database and API goes to Andreas Kahari of the Ensembl Software team.
Ensembl Events in June 2009
For June we have the following Ensembl events:
4-5 June : Browser workshop at the University of Cambridge, Cambridge, UK
11 June: Demo for the National Genetics Reference Lab, Manchester, UK
15-16 June: Browser workshop at the Facultad de Ciencias de la Universidad de Los Andes, Mérida, Venezuela
18-19 June: Developers workshop at the Facultad de Ciencias de la Universidad de Los Andes, Mérida, Venezuela
22 June: Browser workshop for NHS Molecular Genetics Laboratories at Liverpool Women’s Hospital, Liverpool, UK
24-26 June: Ensembl module in the Bioinformatics for Vascular Biology course at the EBI, Hinxton, UK
29 June: Browser workshop at the Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.
Ensembl Events in May 2009
For May we have the following Ensembl events:
29 April – 1 May: Ensembl Developers workshop at the University of Cambridge, Cambridge, UK
8 May: Browser workshop at Imperial College, London, UK
11-13 May: Ensembl module in the Wellcome Trust Open Door Workshop – Working with the Human Genome Sequence, Hinxton, UK
11-15 May: Ensembl module in the EBI hands-on training A walktrough EBI Bioinformatics Resources, Hinxton, UK
12-13 May: Ensembl module in the EBI roadshow at the Université Victor Segalen Bordeaux 2, Bordeaux, France
19-21 May: Ensembl module in the EBI roadshow at the Universidade de Santiago de Compostela, Santiago de Compostela, Spain
22 May: Browser workshop at the European Human Genetics Conference, Vienna, Austria
26 May: Ensembl Developers workshop at the VIB Flanders Interuniversity Institute of Biotechnology, Ghent, Belgium
27-28 May: Browser workshop at the Erasmus MC Molecular Medicine Postgraduate School, Rotterdam, The Netherlands
For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.
Ensembl Genomes live!
Today the long-awaited Ensembl Genomes went live! This is a ‘sister project’ focusing on those species that aren’t part of Ensembl, i.e. non-vertebrates. Please have a look at what the Ensembl Genomes team have to say about it themselves:
“We are delighted to announce the forthcoming release of Ensembl Bacteria, Ensembl Protists and Ensembl Metazoa, the first sites to be launched as part of the EBI’s “Ensembl Genomes” project to extend the use of the Ensembl browser to non-vertebrate genomes.
These following site are available:
http://bacteria.ensembl.org
http://protists.ensembl.org
http://metazoa.ensembl.org
Additional sites for fungi and plants are in development and will be launched during the summer of this year.
In the Ensembl Genomes project, we are aiming to do two things: firstly to work with particular communities to support the bioinformatic analysis of genome-scale data; and secondly, to provide an integrative portal to data from species of scientific interest from across the taxonomic space. In pursuit of both these aims, we will re-use and extend the proven Ensembl software system, that has been developed by EBI and the Wellcome Trust Sanger Institute in the context of vertebrate genomics.
As with Ensembl, Ensembl Genomes will provide access to DNA and protein sequence, positional and functional annotation of protein-coding and non-protein coding genes, repeat analysis and other features and statistics. An interesting feature made available with the release of Ensembl Genomes is the inclusion of a multi-way comparative genomic analysis performed using a selection of species from bacteria to humans, and the production of gene trees showing the inferred ancestral relationships within deeply conserved protein families. Comparative resources are also provided at a narrower level (for example, DNA and protein-based analyses of individual bacterial clades). In partnership with collaborators, we are working on capturing gene expression, and population-scale variation data, in a number of contexts. More generally, we anticipate the ongoing enrichment of these resources through the integration of increasing quantities of high throughput data now becoming routinely available for all species.
Ensembl Genomes will provide access to data through the usual routes supported for vertebrate data; web-based browser, FTP site, programmatic API, DAS, and BioMart-style data warehouse; as well as text and sequence-based search.
We look forward to working with you as future producers and consumers of data. More information about the project is available at http://www.ensemblgenomes.org. We will be happy to receive any feedback you might wish to offer us at helpdesk@ensemblgenomes.org.”
Ensembl Events in April 2009
For April we have the following Ensembl events:
31 March – 1 April : Browser workshop at the IGC, Oeiras, Portugal
2-3 April: Ensembl Developers workshop at the IGC, Oeiras, Portugal
16 April: Demo for the National Genetics Reference Lab, Manchester, UK
17 April: Browser workshop at Imperial College, London, UK
22 April: Browser workshop at Imperial College, London, UK *postponed to 8 May*
27-29 April: Ensembl module in the EBI roadshow at the University of Iceland, Reykjavik, Iceland
27-29 April: BioMart module in the EBI hands-on training Programmatic Access to Biological Databases (Java), Hinxton, UK
29 April – 1 May: Ensembl Developers workshop at the University of Cambridge, Cambridge, UK
For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.
Upcoming workshops February 2009
In February we will have the following Ensembl workshops:
10 Feb: Browser workshop at the Institute for Animal Health in Pirbright
11 Feb: Browser workshop at the Institute of Molecular Genetics in Prague, Czech Republic
12 Feb: Developers workshop at the Institute of Molecular Genetics in Prague, Czech Republic
23 Feb: Ensembl module in the EBI Roadshow at the Cyprus Institute of Neurology & Genetics in Nicosia, Cyprus
24-25 Feb: Developers workshop at the e-Science Centre in Edinburgh
26 Feb: Browser workshop at the Institute for Animal Health in Compton
For details about these and other upcoming workshops, please have a look at the complete list of Ensembl training events.
Upcoming training events December
There are still a few more Ensembl training events before the end of the year.
Browser workshops:
UNAM, Mexico City, Mexico (1-2 Dec)
UNAM, Cuernavaca, Mexico (5 Dec) (+ departmental seminar 4 Dec)
Amsterdam, The Netherlands (19 Dec)
Developers workshop:
University of Cambridge, UK (1-3 Dec)
In addition, Ensembl will feature as part of the following courses:
Wellcome Trust Open Door Workshop ‘Working with the Human Genome Sequence’ (1-2 Dec, Hinxton, Cambridge, UK) and Genes en evolución, ecologia e conservación (8-9 Dec, La Paz, Baja California, Mexico)
For details of these workshops, please have a look at the complete list of Ensembl training events.
Upcoming training events November
Only 3 continents to cover this time, but November will be even busier for the Ensembl trainers than October ….
Ensembl will feature as part of the following courses:
‘Computational & Comparative Genomics’ (5-11 Nov, Cold Spring Harbor Laboratory, New York, US)
Wellcome Trust Open Door Workshop ‘Working with the Human Genome Sequence (10-12 Nov, Wellcome Trust Genome Campus, Hinxton, UK)
Hands-on training at EBI ‘Programmatic access in Java: webservices & work flows’ (24-27 Nov, Wellcome Trust Genome Campus, Hinxton, UK)
Browser workshops will be given at the following locations:
Europe:
Prague, Czech Republic (2 Nov)
Madrid, Spain (5 Nov)
Newcastle, UK (13 Nov)
Cambridge, UK (13-14 Nov)
Naples, Italy (19 Nov)
North America:
Cambridge, Massachusetts, US (12 Nov & 14 Nov)
Boston, Massachusetts, US (13 Nov)
Asia:
Kuala Lumpur, Malaysia (24-25 Nov)
Sabah, Malaysia (27-28 Nov)
For details of these workshops, please have a look at the complete list of Ensembl training events.
Upcoming training events October
As usual October is a busy month for the Ensembl trainers with workshops on 4(!) different continents.
From 1-3 Oct Ensembl will feature in the Wellcome Trust Open Door Workshop “Working with the Human Genome Sequence” in Hyderabad, India, and from 6-8 Oct in the EBI hands-on workshop “A two-day dip into the EBI’s data resources: Understanding your data” in Hinxton, UK.
Upcoming browser workshops:
9-10 Oct: J. Craig Venter Institute, Rockville, MD, US
14 Oct: National Human Genome Research Institute (NHGRI), Bethesda, MD, US
15 Oct: National Human Genome Research Institute (NHGRI), Bethesda, MD, US
16-17 Oct: University of the Free State, Bloemfontein, South Africa
20-21 Oct: University of the Witwatersrand, Johannesburg, South Africa
22 Oct: University of Nottingham, Nottingham, UK
23-24 Oct: University of the Western Cape, Cape Town, South Africa
29-30 Oct: EBI Roadshow, Dublin, Ireland
If you want to know to which locations we are coming after October, then have a look at the complete list of all upcoming training events.
Considering hosting an Ensembl workshop yourself? Please contact Xose Fernandez.