Transcript An Introduction to the EBI and course expectations

The EMBL-European Bioinformatics Institute
The hub for bioinformatics in Europe
Dr Laura Emery
[email protected]
www.ebi.ac.uk
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 European Molecular Biology Laboratory
Heidelberg
Hamburg
Hinxton, Cambridge
Basic research
Administration
EMBO
Structural biology
Bioinformatics
Grenoble
Monterotondo, Rome
Structural biology
Mouse biology
EMBL staff:
1500 people
>60
nationalities
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
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
Services
Data and tools for molecular life science
www.ebi.ac.uk/services
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
Share it with
other data
providers
Classify it
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
Chemical biology
•
•
•
ChEBI
ChEMBL
Patent compounds
Cross-domain resources
• Europe PubMed Central
• Gene Ontology
Systems
•
•
•
BioModels
BioSamples Database
Enzyme Portal
Molecular & cellular structure
• Protein Data Bank in Europe
• Electron Microscopy Data Bank
Reactions,
interactions &
pathways
•
•
IntAct
Reactome
Where to start?
use Firefox
or Google
Chrome
Search here
The EBI Search Service
Gene and protein summaries
Explore the data and
return easily to
your results
Data organised by:
• gene
• expression
• protein
• structure
• literature
Species selector
allows for easy
comparison
The EBI Search Service
Gene and protein summaries
Species selector
allows for easy
comparison
Data organised by:
• gene
• expression
• protein
• structure
• literature
Explore the data and
return easily to
your results
Accessing our services
the services tab
programmatic
access
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
Download FASTA
files for chosen
sequences
www.ebi.ac.uk/ena
Ensembl
• Explore human, mouse and other chordate (and selected
invertebrate) genomes
Gene models
Comparative data
Browse a genomic region
gene trees,
homologues,
alignments, synteny
Sequences
genomes, genes,
transcripts, proteins
Regulatory
data
ENCODE
www.ensembl.org
Variation data
Tools
short and structural
variants, phenotypes
BLAST/BLAT sequence
search,
Variant Effect Predictor
Access: website, BioMart, Perl and REST API
Ensembl Genomes
• Explore genome-scale data from bacteria, protists, fungi,
plants and invertebrate metazoan
Genome portals
for the five
kingdoms of life
Variation data for plant,
metazoan and fungal
species
Pan-taxonomic
comparative
analysis
Multi-way
comparison of
whole bacterial
chromosomes
Access: website, BioMart, Perl and REST API
www.ensemblgenomes.org
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
Read descriptions of sample
properties
www.ebi.ac.uk/arrayexpress
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
Baseline Atlas
Prototype
www.ebi.ac.uk/gxa
Bioinformatics tools
• Over 100 analysis tools
• Results enriched with data from EBI resources
Nucleotide sequence search
Protein sequence search
e.g. BLAST nucleotide
e.g. BLAST protein, PSI-Search
Multiple sequence alignment Pairwise sequence
e.g. Clustal Omega, MUSCLE
alignment
e.g. Needle
Protein functional analysis
Functional genomics tools
e.g. InterProScan
e.g. Expression Atlas
Molecular structure analysis
Text mining
e.g. PDBeFold
e.g. EBIMed, Whatizit
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
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
• www.ebi.ac.uk/tools/webservices
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
www.ebi.ac.uk/support/
Research
Data-driven discovery
PhD and postdoctoral programmes
www.ebi.ac.uk/research
Research themes
Genomes
• Nick Goldman
• Ewan Birney
• Paul Flicek
Chemical biology
Transcriptome
s
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•
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Anton Enright
John Marioni
Oliver Stegle
Alvis Brazma
Proteins & structures
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Janet Thornton
Pedro Beltrao
Alex Bateman
Gerard Kleywegt
• Christoph Steinbeck
• John Overington
Pathways &
systems
• Paul Bertone
• Julio Saez-Rodriguez
• Sarah Teichmann
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
PhDs and Postdocs
• EMBL International PhD programme:
www.embl.de/training/eipp
• Postdoctoral positions available from: www.ebi.ac.uk/jobs
• Postdoctoral fellowships:
• EIPOD EMBL sponsored: interdisciplinary
• ESPOD EBI–Sanger: combined experimental/computational
User training
For scientists working at all levels
www.ebi.ac.uk/training
Bioinformatics training
Train at EMBL-EBI
Train at your place
Gain hands-on
Choose the training that’s
experience in our state-ofright for you and your
the-art facilities.
colleagues - and our
experts will come to you.
www.ebi.ac.uk/training
Train online
Learn in your own time,
at your own pace with
our freely available
online courses.
Train online
• Free online courses
• Learn in your own time,
at your own pace
• Created for life-science
researchers
• No previous knowledge
of bioinformatics
needed
www.ebi.ac.uk/training/online
With thanks to our funders
• EMBL member states
• The European Commission
• The Wellcome Trust
• Research Councils UK
• US National Institutes of Health
Thank you!
www.ebi.ac.uk
Twitter: @emblebi
Facebook: EMBLEBI
YouTube: EMBLMedia