Training

Cross-domain tools and resources

• Learn how to navigate the EBI website and the different ways to access and retrieve data
• Appreciate the depth and variety of tools and databases available at EMBL-EBI
• Gain a brief overview of the major databases at EMBL-EBI

• Understand the basics of sequence similarity searching and sequence homology
• Learn how to find sequences across the whole of EMBL-EBI
• Learn about the different sequence similarity searching tools available at EMBL-EBI (including BLAST, FASTA and PSI-BLAST) and which ones are appropriate for different applications

DNA & RNA

• Appreciate the differences between the major nucleotide sequence databases
• Browse the ENA database in detail, learning about its structure and the type of data it contains
• Select the most appropriate way to access sequence data for a specific purpose (DBFetch, ENA browser...)

This interactive module offers participants hands-on experience in the use of the Ensembl genome browser. Supporting over 60 species, Ensembl provides access to the human, mouse, zebrafish and other (mostly vertebrate) genomes. We will customise the module to provide an overview of a selection of the following:

• How to view genes
• SNPs and other sequence variants and associated phenotypes
• Multi-species comparisons
• Potential sequences involved in gene regulation (for example from ENCODE data)
• Uploading your own custom data for display
• Introduction to BioMart, a quick data-mining tool

Gene expression

• Learn how to browse and retrieve data from the ArrayExpress public repository of transcriptomics data
• Link to external data analysis tools: R and GenomeSpace
• Data formats for transcriptomics data and submission to ArrayExpress can be covered in a separate lecture

• Understand how to browse and retrieve data from the Expression Atlas, a large-scale meta-analysis of public gene expression data
• Query for condition-specific gene-expression patterns as well as broader exploratory searches for biologically interesting gene/sample correlations
• Browse the Baseline Expression Atlas, a highly curated set of RNA-seq experiments providing information about basal expression in 'normal' tissues
• Appreciate how microarray and RNA-seq data are analysed to build an expression atlas

Expression Atlas

Baseline Expression Atlas

Proteins

• Appreciate the differences between the major protein sequence databases
• Browse the UniProt database in detail, learning about its structure and the type of data it contains
• Select the most appropriate way to access sequence data for a specific purpose (sequence search, text search...)

• Understand the specialised sequence search tools within the InterPro database and how they are used to predict protein classification and function
• Browse the InterPro database, learning about the type of annotation it contains

• Query for enzymes and proteins with enzyme activity using species, compounds and disease 
• Extract information on protein structures, protein sequence, small molecules, reactions and pathways
• Identify diseases associated with a specific enzyme
• Understand how to navigate and use enzyme resources at EMBL-EBI

Enzyme Portal
Reactome
Rhea
IntEnz

Structures

• Understand how to search, retrieve and assess the quality of structural data from the PDB archive
• Predict the probable quaternary assembly of a structure and identify structurally similar interfaces and assemblies
• Learn how to assess protein-ligand interactions and analyse binding sites to identify features important to ligand binding
• Learn how to identify structurally similar proteins, perform a 3D alignment and comparison and visualise the best superimposed models

Systems

• Understand what is to be found in a molecular interaction database, alternative data formats and the various tools designed to work with them
• Learn how to explore reactions and pathways 
• Gain familiarity with specialised tools, such as analysis of expression data

IntAct
Reactome

Chemical biology

• Learn how to search for small molecules and understand their chemical ontology and associated bioactivity data
• Learn about structure representation and search algorithms
• Understand how to extract bioactivity data to construct potential  structure-activity relationships
• Learn how to assess protein-ligand interactions and analyse binding sites to identify features important to ligand binding.

ChEMBL
ChEBI
PDBe

Ontologies

• Discover what the Gene Ontology is and how it is structured
• Appreciate basic ontological concepts
• Learn how gene products are annotated to the Gene Ontology and how to access GO annotations
• Appreciate some of the practical uses of GO for researchers

Cross-domain tools and resources

• Understand the principals of sequence similarity searching and sequence homology
• Learn how to find sequences across the whole of EMBL-EBI
• Learn about the different sequence similarity searching tools available at EMBL-EBI (including BLAST, FASTA and PSI-BLAST) and which ones are appropriate for different applications
• Learn about the algorithms used by different tools, including the differences between local and global alignments, optimal and heuristic tools and profile-based methods
• Learn about pairwise and multiple sequence alignments and the tools available at EMBL-EBI (including ClustalW2 and Clustal Omega)
• Learn how different techniques can be combined in an analysis workflow

Sequence similarity searching
Pairwise sequence alignment
Multiple sequence alignment

DNA & RNA

This interactive module offers participants hands-on experience in the use of the Ensembl genome browser. Supporting over 60 species, Ensembl provides access to the human, mouse, zebrafish and other (mostly vertebrate) genomes. We will customise the module to provide an overview of any of the following:

• How to view genes
• SNPs and other sequence variants and associated phenotypes
• Multi-species comparisons
• Potential sequences involved in gene regulation (for example from ENCODE data)
• Uploading your own custom data for display
• Introduction to BioMart, a quick data-mining tool.

• Learn about genome annotation with a focus on bacteria, protists, fungi, plants and invertebrate metazoa
• Gain practical experience of data mining approaches based on BioMart
• Interpret comparative genomics data (gene trees and homologies) and sequence variation data across populations

Proteins

• Browse and retrieve data from the PRIDE public repository of proteomics data
• Gain practical experience in querying the database and extracting information about identifications of proteins, peptides and protein modifications
• Gain awareness of three PRIDE auxiliary projects: OLS (ontology lookup service), PICR (Protein Identifier CrossReference service) and DoD (Database On Demand)

Structures

• Understand how to search, retrieve and assess the quality of structural data from the PDB archive
• Predict the probable quaternary assembly of a structure and identify structurally similar interfaces and assemblies
• Learn how to assess protein-ligand interactions and analyse binding sites to identify features important to ligand binding
• Learn how to identify structurally similar proteins, perform a 3D alignment and comparison and visualise the best superimposed models

Chemical biology

• Learn how to search for small molecules and understand their chemical ontology and associated bioactivity data 
• Learn about structure representation and search algorithms
• Understand how to extract bioactivity data to construct potential structure activity relationships
• Learn how to assess protein-ligand interactions and analyse binding sites to identify features important to ligand binding