1. The EMBL-European Bioinformatics Institute
The hub for bioinformatics in Europe
Dr Laura Emery

2. What is EMBL-EBI? Part of the European Molecular Biology Laboratory
International, non-profit research institute
Europe’s hub for biological data, services and research
The EBI is based on the Wellcome Trust Genome Campus in Hinxton, which is near Cambridge in UK. The EBI is part of the European Molecular Biology Laboratory and as part of that, we’re a non-profit organisation.

3. The European Molecular Biology Laboratory
Heidelberg
Basic research
Administration
EMBO
Hamburg
Structural biology
Hinxton, Cambridge
Bioinformatics
Grenoble
Structural biology
Monterotondo, Rome
Mouse biology
EMBL staff:
1500 people
>60 nationalities
We’re the second largest of the five EMBL sites; there is the main lab and administrative centre in Heidelberg; structural biology labs in Hamburg and Grenoble; mouse biology in Monterotondo, near Rome, and bioinformatics in Hinxton. There are around 1,500 staff within EMBL and about 520 of those work at the EBI.

4. EMBL-EBI’s mission
Provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress
Contribute to the advancement of biology through basic investigator-driven research in bioinformatics
Provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators
Help disseminate cutting-edge technologies to industry
Coordinate biological data provision throughout Europe
The EBI is at the centre of Europe’s efforts to collect, organise and make available all types biological data
We do this by providing services so researchers can access and make sense of the information, by being active in bioinformatics research, by providing training and by working closely with industry.

5. EMBL member states
Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom Associate member state: Australia
We’re the second largest of the five EMBL sites; there is the main lab and administrative centre in Heidelberg; structural biology labs in Hamburg and Grenoble; mouse biology in Monterotondo, near Rome, and bioinformatics in Hinxton. There are around 1,500 staff within EMBL and about 520 of those work at the EBI.

6. Data and tools for molecular life science
Services
Data and tools for molecular life science

7. What services do we provide?
Labs around the world send us their data and we…
…provide tools to help researchers use it
A virtuous circle
Archive it
Analyse it
Classify it
Share it with other data providers

8. Data resources at EMBL-EBI
Genes, genomes & variation
European Nucleotide Archive (ENA)
EBI Metagenomics
Ensembl
Ensembl Genomes
European Genome– phenome Archive
Non-redundant patent sequence databases
Proteins
UniProt: the Universal Protein Resource
InterPro
Pfam
Expression
ArrayExpress
Expression Atlas
MetaboLights
PRIDE
Molecular & cellular structure
Protein Data Bank in Europe
Electron Microscopy Data Bank
Chemical biology
ChEBI
ChEMBL
Patent compounds
Reactions, interactions & pathways
IntAct
Reactome
The slide shows the core resources at the EBI to show the range of data you can access through the EBI.
Cross-domain resources
Europe PubMed Central
Gene Ontology
Systems
BioModels
BioSamples Database
Enzyme Portal

9. use Firefox or Google Chrome
Where to start?
use Firefox or Google Chrome
Search here

10. The EBI Search Service Gene and protein summaries
Explore the data and return easily to
your results
Species selector allows for easy comparison
Data organised by:
gene
expression
protein
structure
literature
The EBI has a new, ‘biologically aware’ search service that we developed in response to the needs of our bench-biologist users. Our intuitive, ‘biologically aware’ search service provides a huge simplification for users exploring the data. For example, if you enter p53 in the search box, you are most likely looking for the (human) p53 gene, rather than the gene encoding a p53-binding protein or a p53-like protein; the new search engine takes this into account, and ranks the results accordingly.
From an uncluttered results 'dashboard', you can explore genes, protein sequences, gene expression, molecular structures and the scientific literature. You can still delve into the individual databases and the original experimental data, but can return easily to the results summary. A species selector allows you to compare key information for human, mouse, fly and other species, and the literature results include links to free full-text articles.

11. The EBI Search Service Gene and protein summaries
Species selector allows for easy comparison
Data organised by:
gene
expression
protein
structure
literature
The EBI has a new, ‘biologically aware’ search service that we developed in response to the needs of our bench-biologist users. Our intuitive, ‘biologically aware’ search service provides a huge simplification for users exploring the data. For example, if you enter p53 in the search box, you are most likely looking for the (human) p53 gene, rather than the gene encoding a p53-binding protein or a p53-like protein; the new search engine takes this into account, and ranks the results accordingly.
From an uncluttered results 'dashboard', you can explore genes, protein sequences, gene expression, molecular structures and the scientific literature. You can still delve into the individual databases and the original experimental data, but can return easily to the results summary. A species selector allows you to compare key information for human, mouse, fly and other species, and the literature results include links to free full-text articles.
Explore the data and return easily to
your results

12. Accessing our services
the services tab
programmatic access

13. European Nucleotide Archive
Comprehensive catalogue of nucleotide sequence data
Covers raw reads, sequence assembly and functional data
Search for DNA sequence
Locate gene sequences
Submit data to the archive
ENA is part of the International Nucleotide Sequence Database Collaboration (INSDC). Comprised of EMBL-Bank, the Short Read Archive (SRA) and the Trace Archive, ENA contains
Download FASTA files for chosen sequences

14. Browse a genomic region
Ensembl
Explore human, mouse and other chordate (and selected invertebrate) genomes
Gene models
Comparative data
gene trees, homologues, alignments, synteny
Browse a genomic region
Sequences
genomes, genes, transcripts, proteins
Ensembl provides a framework for working with the genomes of higher animals (metazoans).
It presents, via an interactive website, the human genome together with other genomes that are important for addressing questions in medical research and molecular biology.
It uses automated methods for gene prediction and annotation to provide a consistent view of completely sequenced genomes.
Users can view the data at many levels, from entire chromosomes down to single nucleotide polymorphisms.
As well as accessing a wealth of data for each species, users can also perform cross-species comparisons.
Variation data
short and structural variants, phenotypes
Tools
BLAST/BLAT sequence search,
Variant Effect Predictor
Regulatory data
ENCODE
Access: website, BioMart, Perl and REST API

15. Ensembl Genomes
Explore genome-scale data from bacteria, protists, fungi, plants and invertebrate metazoan
Variation data for plant, metazoan and fungal species
Genome portals for the five kingdoms of life
Pan-taxonomic comparative analysis
Multi-way comparison of whole bacterial chromosomes
Ensembl Genomes is the combined repository for non-vertebrate genome data, consisting of five resources: Ensembl Bacteria, Ensembl Fungi, Ensembl Metazoa, Ensembl Plants, and Ensembl Protists, bringing the power of the Ensembl system to all branches of life.
Ensembl Genomes re-uses and extends software developed for vertebrate genomes in the context of the Ensembl project, and replaces several pre-existing resources (Genome Reviews and ASTD) thereby unifying services and simplifying data access for users.
Access: website, BioMart, Perl and REST API

16. ArrayExpress
Archive of functional genomics data – RNA-Seq, ChIP- Seq and array-based technologies
MIAME- and MINSEQE- standard compliant
Search experiments
Expand results
Apply filters to refine a search
ArrayExpress is the world’s first and largest MIAME-compliant repository for microarray-based data (mostly gene expression data, but it also takes CGH and chip-chIP data). You can search the repository to view and download experiments; a subset of the data in the repository is hand-picked for the Data Warehouse, which can be searched on the basis of gene names and allows you to view gene expression data for different time points or experimental conditions.
Read descriptions of sample properties

17. Expression Atlas A curated subset of the ArrayExpress data
Search for gene expression changes under different biological/experimental conditions.
Gene page
Search by gene, organism and/or biological condition
Contains and analysed subsets of the array express data
It has been analysed to report differential expression genes
Current expression Atlas reports relative expression levels
The new baseline Atlas is only based on RNA-seq data and reports absolute expression level
You can search for a gene, and then you'll see a heat maps to show whether it's under expressed or overexpressed in each of the different conditions listed horizontally
ArrayExpress is the world’s first and largest MIAME-compliant repository for microarray-based data (mostly gene expression data, but it also takes CGH and ChIP-ChIP data). You can search the repository to view and download experiments; a subset of the data in the repository is hand-picked for the Data Warehouse, which can be searched on the basis of gene names and allows you to view gene expression data for different time points or experimental conditions.
Baseline Atlas Prototype

18. Bioinformatics tools Over 100 analysis tools
Results enriched with data from EBI resources
Nucleotide sequence search
e.g. BLAST nucleotide
Protein sequence search
e.g. BLAST protein, PSI-Search
Multiple sequence alignment
e.g. Clustal Omega, MUSCLE
Pairwise sequence alignment
e.g. Needle
Protein functional analysis
e.g. InterProScan
Functional genomics tools
e.g. Expression Atlas
Molecular structure analysis
e.g. PDBeFold
Text mining
e.g. EBIMed, Whatizit
As well as providing data itself at EMBL-EBI, we also enable you to analyse your own data using our resources and data collections.
The wide-ranging tools are developed internally, externally and by collaboration with leading authors. They are incorporated into our web framework to allow a consistent user experience, access to the latest data and to leverage cross-resource information, for example automatically annotating aligned regions of a BLAST protein search with domain and motif information.
Sequence similarity searching:
Central to genome annotation
Characterising protein families
Exploring distant evolutionary relationships

19. Navigating the EBI EBI resources are linked to one another
Allows you to move to other relevant information
Gain a greater overview of biological applications

20. Programmatic access: EBI Web Services
Run tasks on EBI servers, using EBI data
Ideal for large scale analyses, repetitive tasks and internal pipelines
Integration of EBI resources and data
EBI Search, tools, data retrieval
Same programs, data and results enrichment as running via the web pages
Web Services combines the flexibility of command-line access and scripting with access to our powerful compute and data resources, so you don’t have to worry about maintaining local software or data, you run the latest versions directly on our servers.
Since its introduction, Web Services has become extremely popular: for each job submitted via the web pages more than five times as many jobs are submitted via Web Services.
They’re ideal for all sorts of tasks – large scale analyses, repetitive tasks, internal pipelines, engines behind your own program or web page front end.

21. Getting help EBI resources are vast and very daunting
Don’t worry. We are here to help. Don’t be afraid to ask.
Take a Quick Tour in Train Online
Read resource documentation
Contact EBI Help Desk

22. Data-driven discovery PhD and postdoctoral programmes
Research
Data-driven discovery
PhD and postdoctoral programmes

23. Research themes Genomes Chemical biology Transcriptomes
Nick Goldman
Ewan Birney
Paul Flicek
Chemical biology
Christoph Steinbeck
John Overington
Transcriptomes
Anton Enright
John Marioni
Oliver Stegle
Alvis Brazma
Pathways & systems
Paul Bertone
Julio Saez-Rodriguez
Sarah Teichmann
Here are the research groups at the EBI.
The groups are mapped onto an arrow to demonstrate that our research spans the central dogma of biology - from nucleotides and small RNAs through to genome-scale analysis of regulatory systems.
In the next talk by Anton Enright, you’ll get a more in-depth look at research at the EBI
Proteins & structures
Janet Thornton
Pedro Beltrao
Alex Bateman
Gerard Kleywegt

24. Research at EMBL-EBI Protein targets for new drugs
Molecular basis of ageing
Neurons in Parkinson’s disease
Stem cell differentiation
Cancer genome structure
DNA data storage

25. PhDs and Postdocs
EMBL International PhD programme:
Postdoctoral positions available from:
Postdoctoral fellowships:
EIPOD EMBL sponsored: interdisciplinary
ESPOD EBI–Sanger: combined experimental/computational
PhDs: Visit EMBL Heidelberg for 3 months for the core course: to learn about research in molecular biology and to become familiar with EMBL culture (great way to meet other predocs, as we call them). A mixture of lectures, interactive seminars and hands-on rotations through multiple laboratories at EMBL.
All EBI PhD students are part of the EMBL programme and receive their PhDs from Cambridge.
Active calendar of events, including informal student seminars, visiting speakers, courses, workshops, and of course, social events.
Postdocs are advertised on the jobs pages. We also have two formal fellowship programmes:
1) EIPODs (the EMBL Interdisciplinary Postdoctoral programme) brings together scientific fields that are usually separate or transfer techniques to a novel context.
Each project will have one scientific supervisor who will officially host the EIPOD, but all projects will involve extensive collaboration with the partner labs.
Design and propose your project or select from a list of pre-designed projects.
2) ESPOD (EBI-Sanger postdoctoral) programme. This builds on our strong collaborative relationships between the two institutions and provides the opportunity to combine experimental and computational approaches. Projects may be selected from predefined areas or proposed by the applicant. Each fellowship will last three years and there will be two such fellowships this year.

26. For scientists working at all levels
User training
For scientists working at all levels

27. Bioinformatics training
Train at EMBL-EBI
Gain hands-on experience in our state-of-the-art facilities.
Train at your place
Choose the training that’s right for you and your colleagues - and our experts will come to you.
Train online
Learn in your own time, at your own pace with our freely available online courses.

28. Train online www.ebi.ac.uk/training/online Free online courses
Learn in your own time, at your own pace
Created for life-science researchers
No previous knowledge of bioinformatics needed

29. With thanks to our funders
EMBL member states
The European Commission
The Wellcome Trust
Research Councils UK
US National Institutes of Health

30. Thank you! www.ebi.ac.uk Twitter: @emblebi Facebook: EMBLEBI
YouTube: EMBLMedia