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Learning and exploring Life science through the EBI reosurces and tools
BIOQUEST workshop_2011
Vicky Schneider, EMBL-EBI Training Programme Project [email protected]
19.04.232
What is EMBL-EBI?
• Based on the Wellcome Based on the Wellcome Trust Genome Campus near Trust Genome Campus near Cambridge, UKCambridge, UK
• Part of the European Part of the European Molecular Biology Molecular Biology LaboratoryLaboratory
• Non-profit organisationNon-profit organisation
3
What is bioinformatics?
19.04.234
What is bioinformatics?
storing retrieving analysing
InterdisciplinaryHeart of
modern biology
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Biology is changing
• Data explosion
• New types of data
• High-throughput biology
• Emphasis on systems, not reductionism
• Growth of applied biology
• molecular medicine
• agriculture
• food
• environmental sciences…
Growth of raw storage at EMBL-EBI(in terabytes)
The molecules of life
19.04.236
The ‘book of life’DNA contains the
information needed to build an organism
The ‘book of life’DNA contains the
information needed to build an organism
The interpreterRNA translates the DNA code into protein
The interpreterRNA translates the DNA code into protein
Molecular machinesProteins carry out the functions of life: Catalysts: enzymes enable reactions to
occur at body temperatureStructural support: keratin and collagen
give structure to our tissuesTransport: carrier proteins move molecules
into and out of cellsDefense: antibodies protect us from
disease-causing organismsMovement: myosin in muscles enables
them to contract
Molecular machinesProteins carry out the functions of life: Catalysts: enzymes enable reactions to
occur at body temperatureStructural support: keratin and collagen
give structure to our tissuesTransport: carrier proteins move molecules
into and out of cellsDefense: antibodies protect us from
disease-causing organismsMovement: myosin in muscles enables
them to contract
Nature’s ingredientsSmall molecules provide
building blocks, messengers and helpers:
Amino acids: the building blocks of proteinsNucleotides and sugars: the building blocks of DNA and RNACo-enzymes: pigments such as chlorophyll and haem help imprortant processes such as photosynthesis and respirationHormones: small molecules such as adrenalin and testosterone send important messages from cell to cell
Nature’s ingredientsSmall molecules provide
building blocks, messengers and helpers:
Amino acids: the building blocks of proteinsNucleotides and sugars: the building blocks of DNA and RNACo-enzymes: pigments such as chlorophyll and haem help imprortant processes such as photosynthesis and respirationHormones: small molecules such as adrenalin and testosterone send important messages from cell to cell
Bioinformatics underpins life-science research
1 GenomesContain genes
1 GenomesContain genes
2 Genes are transcribed
2 Genes are transcribed
5 Proteins interact with each other and with small molecules to
form pathways
5 Proteins interact with each other and with small molecules to
form pathways
3 Transcripts translate to protein sequences
3 Transcripts translate to protein sequences
4 Proteins form three-dimensional structures
4 Proteins form three-dimensional structures
6 Pathways combine to build systems
6 Pathways combine to build systems
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From molecules to medicineMolecular components Integration Translation
Genomes
Nucleotides
Transcripts
Proteins
Complexes
Pathways
Small molecules
Structures
Domains
Cells
Biobanks
Tissues and organs
Humanpopulations
Therapies
Diseaseprevention
EarlyDiagnosis
Humanindividuals
Example of the importance of biological information to all of us
Genome-wide analysis of crop plants
• Population growth and climate change are major challenges to food security.
• Traditional routes to crop improvement are too slow to keep up with this increase in demand.
• Understanding plant genomes helps us identify which species will be most tolerant to drought, salt and pests while still providing optimum nutrition.
Matching the treatment to the cancer
• One in ten women in the EU-27 will develop breast cancer before the age of 80.
• If we can identify patterns of genes that are active in different tumours, we can diagnose and treat cancers earlier.
Tracking the source of infectious disease
• Methicillin-resistant MRSA (Staphylococcus aureus) infection is a global problem.
• Transmission of individual clones can be tracked using small variations in DNA sequence.
• This technology can be used to identify the source of new outbreaks across continents and within wards.
Barcoding life
• DNA barcodes are short sections of DNA that we use to identify an organism.
• The Barcode of Life Initiative is developing DNA barcoding as a global standard for identifying species.
• Applications include:
• Protection of endangered species
• Sustaining natural resources through pest control
• Food labelling
Repurposing drugs for neglected diseases
• Schistosomiasis is a parasitic infection that affects 210 million people in 76 countries.
• Resistance is developing to the one available drug.
• We look at the Schistosome genome to identify the targets of existing drugs.
• Candidates can be tested for anti-schistosomal activity or used as leads for further optimisation.
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Lots of data and new types of data
GenomesGenomes
Nucleotide sequenceNucleotide sequence
Gene expressionGene expression
ProteomesProteomes
Protein families, domains and motifs
Protein families, domains and motifs
Protein structureProtein structure
Protein-protein interactions
Protein-protein interactions
Chemical entitiesChemical entities
PathwaysPathwaysSystemsSystems
LiteratureLiterature
Protein sequenceProtein sequence
EMBL-Bank
UniProt
ArrayExpress
Atlas
InterPro
Pfam
Ensembl
PDB
PDBsum
IntAct
Reactome
IntEnz
ProFunc
MACiE
ChEBI
BioModelsGenBank Pubmed
CiteXplore
GO
BLAST
FASTA
CATH
SCOP
PubChem
RefSeq
VAST
GEO
Genomes
Nucleotide Sequences
Protein Sequences
Macromolecular Structures
Small Molecules
Gene Expression
Molecular Interactions
Reactions & Pathways
Protein Families
Enzymes
Literature
Ontologies
Patent Resources
Sequence Similarity & Analysis
Pattern & Motif Searches
Structure Analysis
STRING
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EMBL-EBI
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The five branches of EMBL
Mouse biology
Monterotondo
Structural biology
Grenoble
Bioinformatics
Hinxton
Structural biology
Hamburg
Basic research in molecular biologyAdministrationEMBO
Heidelberg
• 1500 staff
• >60 nationalities
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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
• In 2010 it cost €41 million to run EMBL EBI.
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How is EMBL-EBI funded?
EMBL member states (€22.4 M)EU (€7.4 M)
Charity (€4.1 M)US Govt (€2.9 M)
UK ResearchCouncils (€2.5 M)
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The Wellcome Trust Genome Campus
EMBL-EBI
Sanger InstituteSulston Building
Cairns Pavilion(shared)
Sanger Labs/informatics
Data centre
Sanger Research Support Facility
Thanks to Don Powell, Wellcome Trust Sanger Institute, for providing this image.
EMBL-EBI’s mission statement
• 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
• To coordinate biological data provision across Europe
19/04/23