European Bioinformatics Institute - AbsoluteAstronomy.com

The European Bioinformatics Institute (EBI) is a centre for research and services in bioinformatics

Bioinformatics

Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...

, and is part of European Molecular Biology Laboratory

European Molecular Biology Laboratory

The European Molecular Biology Laboratory is a molecular biology research institution supported by 20 European countries and Australia as associate member state. EMBL was created in 1974 and is an intergovernmental organisation funded by public research money from its member states...

(EMBL). It is located on the Wellcome Trust Genome Campus

Wellcome Trust Genome Campus

The Wellcome Trust Genome Campus is a scientific research campus built in the grounds of Hinxton Hall, located in the village of Hinxton, Cambridgeshire....

in Hinxton

Hinxton

Hinxton is a village in South Cambridgeshire, England. It is the home to the Wellcome Trust Genome Campus, which includes the Wellcome Trust Sanger Institute and the European Bioinformatics Institute. The 2001 population was 315....

, Great Britain

United Kingdom

The United Kingdom of Great Britain and Northern IrelandIn the United Kingdom and Dependencies, other languages have been officially recognised as legitimate autochthonous languages under the European Charter for Regional or Minority Languages...

About the EMBL-EBI

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

Wellcome Trust Genome Campus

The Wellcome Trust Genome Campus is a scientific research campus built in the grounds of Hinxton Hall, located in the village of Hinxton, Cambridgeshire....

in the United Kingdom where it would be in close proximity to the major sequencing efforts at the Sanger Institute

Sanger Institute

The Wellcome Trust Sanger Institute is a non-profit, British genomics and genetics research institute, primarily funded by the Wellcome Trust....

. 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

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

UniProt

UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects...

). Since then, the EMBL-EBI has diversified to provide data resources in all the major molecular domains and expanded to include a broad research base. It provides user support and offers advanced training in bioinformatics.

Funding

As part of EMBL, the largest part of EBI's 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, EBI's 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 EBI's facilities in Hinxton.

Data resources and tools at the EBI

ENA	Genomes	Gene Expression	Literature	Sequence Similarity & Analysis
UniProt	Nucleotide Sequences	Molecular Interactions	Taxonomy	Pattern and Motif Searches
ArrayExpress	Protein Sequences	Reactions and Pathways	Ontologies	Structure Analysis
Ensembl	Macromolecular Structures	Protein Families		Text Mining
InterPro	Small Molecules	Enzymes		Downloads
PDBe	SOAP & REST Web Services	Carbohydrate structures

The EBI acts as a data centre providing several databases and web services:

Full Database and Services indices at the EBI

Groups at the EBI

The EBI hosts many different groups, working on research, providing services to the bioinformatics community or a mixture of both.
EBI Administration (Mark Green)

Bertone Group (Paul Bertone)

Genomic analysis of developmental pathways, with a focus on differentiation and lineage commitment in mammalian embryonic stem cells.

ChEMBL Group (John Overington)

The ChEMBL group's research focuses on mapping the interactions and functional effects of small molecules binding to their macromolecular targets.

Computational Systems Neurobiology Group (Nicolas Le Novère)

The interests of the group Computational Neurobiology revolve around signal transduction

Signal transduction

Signal transduction occurs when an extracellular signaling molecule activates a cell surface receptor. In turn, this receptor alters intracellular molecules creating a response...

in neurons, ranging from the molecular structure

Molecular structure

The molecular structure of a substance is described by the combination of nuclei and electrons that comprise its constitute molecules. This includes the molecular geometry , the electronic properties of the...

of membrane proteins involved in neurotransmission

Neurotransmission

Neurotransmission , also called synaptic transmission, is the process by which signaling molecules called neurotransmitters are released by a neuron , and bind to and activate the receptors of another neuron...

to modelling signalling pathways. A strong focus is the molecular and cellular basis of synaptic plasticity

Synaptic plasticity

In neuroscience, synaptic plasticity is the ability of the connection, or synapse, between two neurons to change in strength in response to either use or disuse of transmission over synaptic pathways. Plastic change also results from the alteration of the number of receptors located on a synapse...

in neurons of the basal ganglia

Basal ganglia

The basal ganglia are a group of nuclei of varied origin in the brains of vertebrates that act as a cohesive functional unit. They are situated at the base of the forebrain and are strongly connected with the cerebral cortex, thalamus and other brain areas...

. The group also provide tools and resources for computational systems biology

Computational systems biology

Modeling biological systems is a significant task of systems biology and mathematical biology.Computational systems biology aims to develop and use efficient algorithms, data structures, visualization and communication tools with the goal of computer modeling of biological systems...

, including the Systems Biology Ontology (SBO), MIRIAM

MIRIAM

MIRIAM , is an effort to standardize the annotation and curation process of quantitative models of biological systems...

Resources, plus software to develop models. A main project of the group is BioModels Database

BioModels Database

BioModels Database is a free and open-source database for storing, exchanging and retrieving published quantitative models of biological interest...

, which allows biologists to store, search and retrieve published mathematical models of biological interest.

Enright Group (Anton Enright)

This group will focus on a number of problems relating to the prediction of the functions of genes and proteins in living organisms.

External Services Group (Rodrigo Lopez)

Develops and maintains Web Services APIs for most tools available from EMBL-EBI, The EB-eye EBI's Search Engine, EBI SRS servers, 2can for external as well as internal users. See also EBI External Services

Ensembl genomes Team (Paul Kersey)

The main focus of the team is currently the development of Ensembl Genomes, the expansion of the use of the Ensembl system from its current focus of vertebrate genomes to cover important species from all domains of life, with the launch of new sites for Ensembl Metazoa, Ensembl Plants and Ensembl Bacteria in late 2008 and Ensembl Plants and Ensembl Fungi in the first half of 2009.

GO Editorial Office (Jane Lomax)

The GO Editorial Office at EBI coordinates the development and maintenance of the GO vocabularies, and contributes to several other GO project efforts, including documentation, web presence, software testing, and user support.

Graham Cameron

Associate Director of the EBI.

Goldman Group (Nick Goldman)

This group is developing methods for the analysis of DNA and amino acid sequences to study evolution.

Huber Group (Wolfgang Huber)

Focuses on gene transcription and protein–DNA binding analysis with DNA microarrays; statistical computing and high-throughput cellular assays and genetic interaction screens.

Industry Support (Dominic Clark)

The EBI supports Industry through two programmes: the EBI Industry Programme is a well established, subscription-based programme for large companies whereas the SME Support Forum offers support to smaller companies that are not eligible to join the Industry Programme.

InterPro Group (Sarah Hunter)

Develops and maintains the InterPro project, an integrated documentation resource for protein families, domains and functional sites that is used for small and large-scale functional classification of proteins.

Literature Services (Peter Stoehr/Johanna McEntyre)

This group is in charge of the development and maintenance of CitExplore and related services.

Regulation Group (Nick Luscombe)

Focuses on the genomic analysis of regulatory systems.

Microarray Group (Alvis Brazma)

Uses microarray technology to analyse the sequence data from the genome projects to identify which genes are expressed in a particular cell type of an organism.

MicroArray Technical Team (Ugis Sarkans)

PDBe - Protein Data Bank Europe (formerly MSD) (Gerard Kleywegt

Gerard Kleywegt

Gerard Kleywegt is an x-ray crystallographer and the team leader of the Protein Data Bank in Europe at the EBI; a member of the Worldwide Protein Data Bank. Gerard Kleywegt obtained his PhD from the University of Utrecht in 1991. After his PhD he studied x-ray crystallography with Alwyn Jones at...

)

Serves a list of protein

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

quaternary structure

Quaternary structure

In biochemistry, quaternary structure is the arrangement of multiple folded protein or coiling protein molecules in a multi-subunit complex.-Description and examples:...

s (or macromolecule

Macromolecule

A macromolecule is a very large molecule commonly created by some form of polymerization. In biochemistry, the term is applied to the four conventional biopolymers , as well as non-polymeric molecules with large molecular mass such as macrocycles...

s) for every entry in the Protein Data Bank

Protein Data Bank

The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....

(PDB) http://www.wwpdb.org/. It is also a member of the Worldwide Protein Data Bank

Worldwide Protein Data Bank

The Worldwide Protein Data Bank, wwPDB, is an organization whose mission, according to its website, is "to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community." Given the open access goal, it is somewhat ironic...

, and is of the three worldwide sites that accept, process and distribute macromolecular structure data. This group aims to improve the consistency and quality of the world archive of data on macromolecular structures by integrating current database and informatics technologies with a solid core of expertise in structural biology. This group also hosts the canonical version of the Eurocarb database

Eurocarbdb

EuroCarbDB is an EU-funded initiative for the creation of software and standards for the systematic collection of carbohydrate structures and their experimental data...

http://www.ebi.ac.uk/eurocarb.

Outreach and Training Team (Cath Brooksbank)

Coordinates firstly communicating the scientific mission and activities of the EBI to the community and secondly the scientific training programme of the EBI. The EBI’s user-training programme equips users of the EBI’s bioinformatics services with the knowledge that they need to use our data resources.

PANDA Protein And Nucleotide DAtabase group Ensembl

Ensembl

Ensembl is a joint scientific project between the European Bioinformatics Institute and the Wellcome Trust Sanger Institute, which was launched in 1999 in response to the imminent completion of the Human Genome Project...

(Rolf Apweiler

Rolf Apweiler

Rolf Apweiler is a senior scientist at the European Molecular Biology Laboratory-European Bioinformatics Institute and joint head of the Protein And Nucleic Acids group with Ewan Birney....

& Ewan Birney

Ewan Birney

Ewan Birney is a senior scientist at the European Bioinformatics Institute and joint head of the Protein And Nucleic Acids group with Rolf Apweiler. The PANDA group is responsible for the widely used Ensembl genome browser, and highly-cited research on, for example, sequence analysis tools...

)

Provides, for almost 35 species, a genome browser, public access to the MySQL

MySQL

MySQL officially, but also commonly "My Sequel") is a relational database management system that runs as a server providing multi-user access to a number of databases. It is named after developer Michael Widenius' daughter, My...

databases of annotations shown in the browser, and a Perl

Perl

Perl is a high-level, general-purpose, interpreted, dynamic programming language. Perl was originally developed by Larry Wall in 1987 as a general-purpose Unix scripting language to make report processing easier. Since then, it has undergone many changes and revisions and become widely popular...

API for accessing the database. The group is divided fairly equally between the EBI and the Wellcome Trust Sanger Institute with gene builders and web team on the Sanger side, and core database and comparative genomics

Comparative genomics

Comparative genomics is the study of the relationship of genome structure and function across different biological species or strains. Comparative genomics is an attempt to take advantage of the information provided by the signatures of selection to understand the function and evolutionary...

teams at the EBI.

Proteomics Services Team (Henning Hermjakob)

Provides databases and tools for the deposition, distribution and analysis of proteomics and proteomics-related data.

Rebholz Group (Dietrich Rebholz-Schuhmann)

Focuses on extraction of facts from scientific literature in molecular biology. The main methods are based on Finite State Automatons (FSAs). In the past has worked on the identification of protein–protein interactions, acronyms and descriptions of mutations.

Rice Group (Peter Rice)

This group is investigating & advising on the e-Science & Grid technology requirements of the EMBL-EBI, through application development plus participation in standards development.

Chemoinformatics and Metabolism (Christoph Steinbeck)

The Steinbeck group's research in molecular informatics focuses on the understanding of the small-molecule metabolism of living organism, including methods for computer-assisted structure elucidation of biological metabolites and simulations of metabolic pathways.

Systems Group (Petteri Jokinen)

Maintains and develops state-of-art computing infrastructure on which most EBI operations are run.

Thornton Group (Janet Thornton)

Using biomolecular structures, tries to understand enzyme active sites, protein–protein interactions, protein–ligand interactions, protein–DNA interactions and structure and modelling.

Vertebrate Genomics Group (Paul Flicek)

This part of the Panda Nucleotides Group (The Vertebrate Genomics Group) focuses on functional annotation of the genome including methods for incorporating high-throughput epigenetic data for expanding and understanding the collection of human variation.

Database Research and Development Group (Weimin Zhu)

The Database Research and Development Group Conduct research and development on the database-related challenges. Biomolecular databases are becoming increasingly large, complex and interconnected. This increase of data scale, complexity and the need of interoperability means that there are many fundamental challenges in the database development, deployment and distribution. The group will be leading the EBI's research into database technologies, looking both at solutions from other fields with similar datasets and examining new, cutting edge technologies from database research.

Education, training and user support

The EBI provides many different education, training, user support and outreach events,
The Bioinformatics Roadshow: a travelling user-training programme that is tailored to the needs of users of Europe’s main data resources.

The EBI Hands-on User Training programme: a series of short courses, held in the EBI’s IT training suite, that aims to familiarise experimental researchers with the EBI’s core data resources.

2can Bioinformatics User Support Portal.

Provides short and concise introductions to basic concepts in molecular and cell biology and bioinformatics. It focuses on making it as easy for the user to understand which tools and databases are available from the EBI and collaborating sites. It also provides links to other sites where similar resources are maintained and well supported.

EBI hosted projects

Several research projects are hosted at the EBI including:

1000 Genomes
BioCatalog
BioSapiens
ENSEMBL - In collaboration with the Wellcome Trust Sanger Institute
Sanger Institute
The Wellcome Trust Sanger Institute is a non-profit, British genomics and genetics research institute, primarily funded by the Wellcome Trust....
E-MeP
ELIXIR
EMBRACE
EMERALD
ENFIN
EuroCarbDB
Eurocarbdb
EuroCarbDB is an EU-funded initiative for the creation of software and standards for the systematic collection of carbohydrate structures and their experimental data...
FELICS
INSDC
SYMBIOmatics
UniProt - In Collaboration with the UniProt consortium: SIB
Swiss Institute of Bioinformatics
The Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland...

, PIR
Protein Information Resource
The Protein Information Resource , located at Georgetown University Medical Center , is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies-History:...

and EBI
Soaplab
Soaplab
Soaplab is a Web Services software framework specialised for bioinformatics programs with command-line interface. It includes a module for running command-line programs as Web Services jobs and provides support to generate Java Web Services web applications for them. It allows both synchronous and...