Introduction and expectations activity

Report
Welcome to EMBL-EBI
Dr Laura Emery
Before we start…
• Stand up
• How experienced are you in bioinformatics?
• Get to know each other by arranging yourselves in order
of your confidence with bioinformatics including using
linux and R
Least
bioinformatics
experience
Most
bioinformatics
experience
Welcome to EMBL-EBI
Useful information while you are here
www.ebi.ac.uk
Genome Campus
EXIT
Registration
desk
EXIT
Welcome to EMBL-EBI
• Contacts
• Training Team – [email protected]
• Registration Desk – 8553
• Emergency – 3333
EXIT
Registration
desk
EXIT
Fire Assembly: Car Park A
Training room rules
Computer workstation
Logging on to your computer
• Your computers should already be logged on
• How to access the Penelope shared drive…
Please remember…
• The room opens at 8:45am each morning
• Sign in at the registration desk each day
• The room locks at 7:00pm each evening
• Fire alarm test at 11:45am Wednesday morning
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
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
ChEBI
• Dictionary of small chemical compounds
• Covers both products of nature and synthetic compounds
Target search
Wikipedia
information
Entity
information
ChEBI
Ontology
Viewer
View
chemical
structure
ChEMBL
• Database of bioactive drug-like molecules
• 2D structure, chemical properties, bioactivity
Target search
Browse
targets
www.ebi.ac.uk/chembl
Compound
search
Reactome
Select a
pathway
Compare events in
different species
Link to source
databases
View reactions and events in
detail
www.reactome.org
Export pathway
to your favourite
modelling
software
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
Getting help
• EBI resources are vast and can be daunting
Take a Quick Tour
in Train Online
Read resource
documentation
Contact EBI Help Desk
www.ebi.ac.uk/support/
User training
For scientists working at all levels
www.ebi.ac.uk/training
Bioinformatics training
Train at EMBL-EBI
Train at your place
Train online
Gain hands-on
experience in our
state-of-the-art
facilities.
Choose the
training that’s right
for you and your
colleagues - and
our experts will
come to you.
Learn in your
own time, at your
own pace with
our freely
available online
courses.
www.ebi.ac.uk/training
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
Expectations activity
• What are your expectations of this course?
• Think to yourself
• Write your thoughts on post-it notes (one expectation per
post-it)
• Discuss these in small groups
• Sort out your post-its to eliminate redundancy
• Nominate a spokesperson to present to the rest of the group
• Stick them on the whiteboards to the right of the room
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

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