EMBL-EBI Workshop: Resources and tools for genomics, protein interactions and structural applications


 Wednesday 20 Thursday 21 February 2019


Università di Pavia - via Ferrata 1, 27100,  Pavia,  PV, Italy


By invitation


Johanna Langrish

Registration closed

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Dates additional information: 

This course runs between 08:30-17:30 for two days, including lunch and refreshment breaks.

Course Overview

In this course participants will explore EMBL-EBI resources for genomics, protein interaction and structural biological applications. The sessions focus on browsing, searching and retrieving genomic data, protein interaction information and three-dimensional structures. 

Day 1 will cover the Ensembl genome browser resource, where researchers can explore annotated genomes and features of interest including genes, s, transcripts, and variants. Participants will also be introduced to the Variant Effect Predictor (VEP) tool and BioMart for bulk data download. 

Day 2 will introduce protein-protein interactions and the molecular interactions and complex databases IntAct and Complex Portal, where researchers can browse, visualize and download protein interaction and complex data. The afternoon sessions will focus on the structural biology archive Protein Data Bank in Europe, where participants can browse and visualize molecular structure data, with an emphasis on the recent Cryo-EM database EMDB/EMPIAR.

The course will be delivered by experienced and dedicated EMBL-EBI trainers, and will involve presentations, demonstrations and practical exercises to give participants hands-on experience.


This course is aimed at researchers at any career stage within the University of Pavia and Institute of Molecular Genetics who are working with and/or generating their own genomic and biomolecular datasets.

No knowledge of programming is required, but an undergraduate level knowledge of Biology / molecular biology would be beneficial.


  • ensemblensembl-genomes
  • interactions-and-pathways
  • introduction-macromolecular-structure-pdbe

Learning outcomes

After this course you should be able to:

  • View genomic regions and manipulate the view to add features you are interested in.
  • Analyse genomic variants and associated phenotypes and your own variation data using the VEP.
  • Explore information about genes and their sequences, and gene data in bulk using BioMart.
  • Describe the data found in molecular interaction and biomolecular complex databases
  • Search, retrieve and assess the quality of structural data from the PDB archive to find the best structure for your needs


Day 1: Genomics resources: Ensembl, VEP, BioMart

Day 2: Protein interactions and structural biology resources: IntAct, Complex Portal, Protein Data Bank in Europe 

Day 1 – Wednesday 20 February 2019
08:30-09:00 Arrival, registration  
09:00-09:30 Welcome and Introduction to EMBL-EBI Resources and Tools Erin Haskell
09:30-11:00 Introduction to Ensembl and browsing the genome browser Erin Haskell
11:00-11:30 Coffee Break
11:30-13:00 Ensembl genes, transcripts and variation data Erin Haskell
13:00-14:00 Lunch
14:00-15:30 The Variant Effect Predictor (VEP) and data export with BioMart Erin Haskell
15:30-16:00 Coffee Break  
16:00-17:30 Comparative genomics or Regulation data Erin Haskell
17:30 End of day 1  
Day 2 – Thursday 21 February 2019
09:00-11:00 Introduction to molecular interactions Birgit Meldal
11:00-11:30 Coffee Break
11:00-12:30 Resources: IntAct and Complex Portal Birgit Meldal
13:00-14:00 Lunch
14:00-15:30 Finding macromolecular structures at PDBe David Armstrong
15:30-16:00 Coffee Break  
16:00-17:30 PDBe tools for understanding macromolecular structures David Armstrong
17:30 Course wrap-up and feedback Birgit Meldal & David Armstrong