Modules

Hosting training at your institute

Would you like EMBL-EBI’s trainers to come to you and teach your researchers how to use the bioinformatics resources most relevant to their research? Contact us to find out more.

Modules

We offer a range of half-day and full-day modules, which can be combined to suit different audiences. Take a look at our modules, or browse upcoming and past workshops (below) for inspiration.

Half-day training modules 

Module Learning objectives Resources and tools covered

 Cross-domain tools and resources

Introduction to databases at EMBL-EBI
  • 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
Various resources and tools
Introduction to sequence searching 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
Sequence Similarity Searching

 DNA & RNA

Nucleotide sequence databases
  • 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...)
ENA (European Nucleotide Archive)
Ensembl and/or Ensembl Genomes browsing 

This interactive module offers participants hands-on experience in the use of the Ensembl and/or Ensembl Genomes genome browsers. Ensembl provides access to the human, mouse, zebrafish and other (mostly vertebrate) genomes, whilst Ensembl Genomes focuses on bacteria, protists, fungi, plants and invertebrate metazoa. 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.

This module can be tailored for species of interest (choosing Ensembl and/or Ensembl Genomes as appropriate), new or frequent users from the wet-lab, or bioinformaticians. Find out more

Ensembl and Ensembl Genomes

 Gene expression

ArrayExpress: public database for transcriptomics data
  • 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

 

ArrayExpress Archive

 

Expression Atlas
  • 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

 

 

 Proteins

Protein sequence databases
  • 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...)
UniProt
Protein function and classification
  • 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
InterPro
Introduction to enzymes and the Enzyme Portal
  • 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

Protein structures and tools from the PDBe 
  • 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
PDBe 

 Systems

Interactions & pathways
  • 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

Complex portal

 Chemical biology

Small molecule resources at EMBL-EBI
  • 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

Standards and 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
GO
OLS

Full-day training modules

Module Learning objectives Resources and tools covered

 Cross-domain tools and resources

Sequence searching and alignments
  • 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

Ensembl and/or Ensembl Genomes browsing

This interactive module offers participants hands-on experience in the use of the Ensembl and/or Ensembl Genomes genome browsers. Ensembl provides access to the human, mouse, zebrafish and other (mostly vertebrate) genomes, whilst Ensembl Genomes focuses on bacteria, protists, fungi, plants and invertebrate metazoa. 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.
This module can be tailored for species of interest (choosing Ensembl and/or Ensembl Genomes as appropriate), new or frequent users from the wet-lab, or bioinformaticians. Find out more
Ensembl and Ensembl Genomes

 Proteins

Mass spectrometry- based proteomics
  • 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)
PRIDE
BioMart
PRIDE Converter
OLS/PICR

 Structures

Protein structures and tools from the PDBe
  • 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
PDBe

 Chemical biology

Small molecule resources at EMBL-EBI
  • 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