http://www.ebi.ac.uk/Information/About_EBI/about_ebi.html
EBIInformationAbout the EMBL-EBI
The history and activities of the EBI:
As we move towards understanding biology at the systems level, access to large data sets of many different types has become crucial. Technologies such as genome-sequencing, microarrays, proteomics and structural genomics have provided ‘parts lists’ for many living organisms, and researchers are now focusing on how the individual components fit together to build systems. The hope is that scientists will be able to translate their new insights into improving the quality of life for everyone. However, the high-throughput revolution also threatens to drown us in data. There is an ongoing, and growing, need to collect, store and curate all this information in ways that allow its efficient retrieval and exploitation. The European Bioinformatics Institute (EMBL-EBI), which is part of the European Molecular Biology Laboratory (EMBL), is one of the few places in the world that has the resources and expertise to fulfil this important task.
The EMBL-EBI lies in the 55 acres of landscaped parkland in rural Cambridgeshire that make up the Wellcome Trust Genome Campus. The Campus also houses the Wellcome Trust Sanger Institute, making it one of the world's largest concentrations of expertise in genomics and bioinformatics. The EMBL-EBI grew out of EMBL's pioneering work to provide public biological databases to the research community (seeHistory). Although we are geographically separated from EMBL's main headquarters in Heidelberg and its other sites in Grenoble, Hamburg and Monterotondo, the EMBL-EBI is an integral part of EMBL. We play a vital role in achieving EMBL's mission of providing a top-quality research environment that also develops new technologies, and provides services and training to Europe's molecular life scientists. Like the other EMBL sites, we have an extremely cosmopolitan staff base, and alumni who have moved on to successful careers all over the world.
To provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress
To contribute to the advancement of biology through basic investigator-driven research in bioinformatics
To provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators
To help disseminate cutting-edge technologies to industry
The roots of the EMBL-EBI lie in the EMBL Nucleotide Sequence Data Library (now known as EMBL-Bank), which was established in 1980 at the EMBL laboratories in Heidelberg, Germany and was the world's first nucleotide sequence database. The original goal was to establish a central computer database of DNA sequences, rather than have scientists submit sequences to journals. What began as a modest task of abstracting information from literature soon became a major database activity with direct electronic submissions of data and the need for highly skilled informatics staff. The task grew in scale with the start of the genome projects, and grew in visibility as the data became relevant to research in the commercial sector. It soon became apparent that the EMBL Nucleotide Sequence Data Library needed better financial security to ensure its long-term viability and to cope with the sheer scale of the task.
There was also a need for research and development to provide services, to collaborate with global partners to support the project, and to provide assistance to industry. To this end, in 1992, the EMBL Council voted to establish the European Bioinformatics Institute and to locate it at the Wellcome Trust Genome Campus in the United Kingdom where it would be in close proximity to the major sequencing efforts at the Sanger Institute. From 1992 through to 1995, a gradual transition of the activities in Heidelberg took place, until in September 1995 the EMBL-EBI occupied its current location on the Wellcome Trust Genome Campus.
When the EMBL-EBI moved to Hinxton it hosted two databases, one for nucleotide sequences (the EMBL Data Library, now known as EMBL-Bank) and one for protein sequences (Swiss-Prot–TrEMBL, now known as UniProt). Since then, the EMBL-EBI has helped to lead the bioinformatics revolution: we have diversified to provide data resources in all the major molecular domains, expanded to include a broad research base, developed unique ways of supporting our users, and we offer advanced training in bioinformatics.
The EMBL-EBI has received over € 32 million in internal and external funding for 2006. The global importance of our work is reflected in the fact that we attracted almost 50% of our funds from external sources, including some beyond Europe.
As part of EMBL, the largest part of our funding comes from the governments of EMBL's 20 member states. Other major funders include the European Commission, Wellcome Trust, US National Institutes of Health, UK Research Councils, our industry partners and the UK Department of Trade and Industry. In addition, the Wellcome Trust generously provides the facilities for the EMBL-EBI on its Genome Campus at Hinxton, and the UK Research Councils have also provided funds for our facilities in Hinxton. 2005 has been an atypical year in that several large external grants have come to an end and new grants, already in the pipeline, have yet to be funded.We thank all our funders for allowing us to continue and expand our work.
Europe has always been at the forefront of bioinformatics research, but as we move towards the European Union's goal of a single European Research Area, there is a greater need than ever for bioinformatics experts and experimental biologists throughout Europe to work together towards common goals that will expedite biological research. To this aim, the EMBL-EBI coordinates three EU-funded Networks of Excellence:
BioSapiens aims to address the current fragmentation of European bioinformatics by creating a virtual research institute for genome annotation and by organizing a European school for training in genome annotation.
EMBRACE will standardise access to bioinformatics resources, enabling data providers to provide well-defined interfaces to their databases that will conform to the same standards. This will allow users to make the most of dispersed data resources.
ENFIN will bring together experimentalists and computational biologists to develop the next generation of informatics resources for systems biology.
Building on more than 20 years' experience in bioinformatics, the EMBL-EBI maintains the world's most comprehensive range of molecular databases.
We are the European node for globally coordinated efforts to collect and disseminate biological data. Many of our databases are household names to biologists – they include EMBL-Bank (DNA and RNA sequences), Ensembl (genomes), ArrayExpress (microarray-based gene-expression data), UniProt (protein sequences), InterPro (protein families, domains and motifs) and PDBe (macromolecular structures). Others, such as IntAct (protein–protein interactions), Reactome (pathways) and ChEBI (small molecules), are new resources that help researchers to understand not only the molecular parts that go towards constructing an organism, but how these parts combine to create systems. The details of each database vary, but they all uphold the same principles of service provision.
Accessibility – We are the custodians (not the owners) of biological data provided by the community, and progress in biological research depends on completely open access to these data. All our data and tools are therefore freely available to the research community, without restriction.
Compatibility – The EMBL-EBI has possibly done more than any other organization in the world to promote the adoption of standards in bioinformatics; the development of these standards promotes data sharing.
Comprehensive data sets – Where several publicly available repositories exist, we have negotiated data-sharing agreements to ensure that our resources contain comprehensive and up-to-date data sets. We also negotiate with publishers to ensure that, wherever practicable, biological data are placed in a public repository as part of the publication process and cross-referenced in the relevant publication.
Portability – All our datasets are available for download. In many cases the entire software system can be downloaded and installed locally.
Quality – Our databases are enhanced through annotation: features of the genes or proteins stored in them are extracted from other sources, defined and interpreted. Much of our annotation is performed by highly qualified biologists, and the automated annotation that we do is subjected to rigorous quality control.
Our External Services team makes our resources available online and provides help to our users. We want to make sure that all our users, who are responsible for over 2.5 million hits on our website each day, have all the information that they need to make the most of our resources. Here's where to start:
New to bioinformatics? Take a look at 2Can Support Portal for background information on the whys and wherefores.
Don't know which service will meet your needs? The Services site map will help you to find the right resource.
Need some hints on how to make the most of the service you're using? Try the help pages.
Can't find the information you need on the help pages? Send us an e-mail and we'll get back to you within two working days.
All our major data resources are the products of international collaborations. We work with other data providers to ensure that our data repositories, and those of our collaborators, are comprehensive and up to date. We actively participate in international efforts to develop data standards; for example:
Our Microarray Informatics team was the driving force behind the development of the MIAME standard, which describes the minimum information required to describe a microarray experiment in an unambiguous way.
Our Proteomics Services team coordinates HUPO's Proteomics Standards Initiative (PSI), which is developing data standards for protein-protein interactions, mass spectrometry, and general proteomics.
Our Computational Neurobiology group is a key player in the development of standards for modeling biological systems, and has contributed to the development of Systems Biology Markup Language(SBML).
We are also proactive in organising events that bring computational biologists from all over Europe and beyond together. More on services
The EMBL-EBI provides a unique environment for bioinformatics research: we have a broad palette of research interests that complement our data resources, and these two strands of activity at the EMBL-EBI are mutually supportive. As an integral part of EMBL – the most productive research institute outside the US – we are an active member of all four of the EMBL Centres, which facilitate interdisciplinary research across EMBL's five sites.
Our research groups aim to understand biology through the development of new approaches to interpreting biological data. Areas of research include: genomic analysis of developmental pathways (Paul Bertone); Evolutionary analysis of sequence data (Nick Goldman); computational systems biology of neuronal signaling (Nicolas Le Novère); Extraction of facts from the scientific literature (Dietrich Rebholz-Schuhmann); Proteomics: structure, function and evolution (Janet Thornton); Genome-scale analysis of regulatory systems (Nick Luscombe); and functional genomics (Wolfgang Huber).
The services teams, who develop and maintain our data resources, also perform research to develop new services and enhance our existing ones. Research carried out in our services teams includes promoter discovery (Ewan Birney); micorarray data analysis and algorithm development (Alvis Brazma), grid- and e-science projects (Peter Rice); and automatic annotation of protein sequence data (Rolf Apweiler). More on research
Bioinformatics is a rapidly expanding discipline that touches on all areas of biology – pure and applied. There is a global shortage of trained bioinformaticians, and the EMBL-EBI fulfils an important function in working towards reducing this shortage.
Graduate training. We have a lively graduate community through EMBL's International PhD Programme. Students can graduate from the university of their choice. Many of the EMBL-EBI's PhD students join the University of Cambridge; they participate fully in Cambridge graduate life and leave the EMBL-EBI with a PhD from the University of Cambridge. The EBI is an affiliated institution of the Graduate School of Biological, Medical and Veterinary Sciences in the School of the Biological Sciences of the University of Cambridge.
Postdoctoral fellowships are available in our research groups. We are classed as an 'academic analogue' in the UK, and can apply to the Wellcome Trust and the UK research councils for funding for postdoctoral fellowships. We encourage potential candidates to contact the group/team leader of their choice to discuss the possibility of doing a post doc at the EMBL-EBI.
Visitors. We also welcome more senior researchers on sabbatical. See our visitors' page for more information.
Training days. We hold training days for masters' and PhD students from other institutions. See ourtraining pages for more information.
We offer support and training to researchers who use our resources: we hold approximately 10 workshops a year as part of our Industry Programme. We also run road shows to train researchers on site at their own institutions; we provide online help pages and e-mail support to our users; and have developed 2Can Support Portal for people who are new to bioinformatics. We are in the process of consolidating our training programme to make bioinformatics training more widely available throughout Europe. More on training
Advances in bioinformatics are having a major impact on industry. We have been supporting the needs of industry for over 9 years through our Industry Programme, which kick-starts research of importance to industry, provides expert training, develops bioinformatics standards, helps its partners with technical development and provides regular networking opportunities. The programme is driven by its partners for its partners, and membership is by invitation. Our industry partners include large multinational companies in the biotech, pharmaceutical, agricultural, nutrition, personal-care and medical devices industries.
The popularity of the EMBL-EBI's industry programme with large pharmaceutical companies has prompted us to consider how we can best serve small-to-medium enterprises (SME's), and we recently launched the EMBL-EBI SME Support Forum. This provides networking opportunities, expert tuition including tailor-made workshops, opportunities for technical development through collaboration, consultancy, and a priority helpdesk. Members can dip into the programme on an ad hoc basis. Members of the SME Support Forum range from drug discovery and biotech start-ups to bioinformatics service providers. More on industry support