Learning and exploring Life science through the EBI reosurces and tools BIOQUEST workshop_2011 Vicky Schneider, EMBL-EBI Training Programme Project leader.

Learning and exploring Life science through the EBI reosurces and tools

BIOQUEST workshop_2011

Vicky Schneider, EMBL-EBI Training Programme Project [email protected]

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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

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What is bioinformatics?

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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

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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

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