EMBL-EBI Workshop: Genomics, transcriptomics and metagenomics tools and resources for biology research


 Tuesday 7 Thursday 9 May 2019


Faculty of Sciences, University of Porto - Rua do Campo Alegre 1021/1055, 4169-007,  Porto, Portugal

Application opens: 

Friday 29 March 2019

Application deadline: 

Sunday 14 April 2019


Open application with selection

Registration fee: 


Registration closed

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Course Overview

This workshop will provide training on computational analysis tools and databases that can be used to answers relevant questions in molecular ecology. Participants will learn how to browse, search and access biological data across the fields of genomics, transcriptomics and metagenomics. Data management and submission strategies using Biostudies will also be covered.

During this course you will learn about:


This course is intended for PhD students of Portuguese and international institutions (with a particular focus on students of the CIBIO-InBIO’s BIODIV, SUSFOR Doctoral Programs and University of Porto), but more experienced researchers that are initiating projects in the field of environmental metagenomics can also participate.
Prerequisite knowledge 
No previous bioinformatics experience is required, but an undergraduate level understanding of biology would be an advantage.


  • ensemblensembl-genomes
  • arrayexpress-public-database-functional-genomics
  • expression-atlas-gene-expression-across-species-and-biological-conditions
  • european-nucleotide-sequence-archive-ena

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
  • Browse the ENA database in detail, learning about its structure and the type of data it contains
  • Access, browse and visualise gene expression data from ArrayExpress and Expression Atlas
  • Use Biostudies to search and quickly access data from a publication
  • Search, browse and download metagenomics data using MGnify


Day 1: Ensembl genome browser
Day 2: ArrayExpress, Expression Atlas
Day 3: Biostudies, European Nucleotide Archive (ENA), ENA for metagenomics, MGnify


Day 1 – Tuesday 7 May 2019
08:30-09:00 Arrival, registration  
09:00-09:15 Introduction to EMBL-EBI Tools and Resources Ben Moore
09:15-11:00 Ensembl genome browser Ben Moore
11:00-11:30 Coffee Break
11:30-13:00 Ensembl genome browser Ben Moore
13:00-14:00 Lunch
14:00-15:30 Ensembl genome browser Ben Moore
15:30-16:00 Break  
16:00-17:30 Ensembl genome browser Ben Moore
17:30 End of day 1  
Day 2 – Wednesday 8 May 2019
09:00-11:00 ArrayExpress Silvie Fexova
11:00-11:30 CoffeeBreak
11:30-13:00 ArrayExpress Silvie Fexova
13:00-14:00 Lunch
14:00-15:30 Expression Atlas Silvie Fexova
15:30-16:00 Coffee Break
16:00-17:30 Expression Atlas Silvie Fexova
17:30 End of day 2  
Day 2 – Thursday 9 May 2019
09:00-10:30 Biostudies webinar Ugis Sarkans and Silvie Fexova
10:30-11:00 Coffee Break
11:00-13:00 European Nucleotide Archive Sam Holt
13:00-14:00 Lunch
14:00-14:45 European Nucleotide Archive for Metagenomics Sam Holt
14:45-15:30 Metagenomics - MGnify Alex Mitchell
15:30-16:00 Coffee Break  
16:00-17:30 Metagenomics - MGnify Alex Mitchell
17:30-17:45 Course wrap-up and feedback Sam Holt and Alex Mitchell

Additional information:

This course is included in the activities planned in the EnvMetagen project. This capacity building project is run at CIBIO-InBIO, a research center in the greater Porto area, and aims to increase expertise and knowledge in the field of environmental metagenomics in Portugal, through a large set of activities that include training in several areas related to this field. Previously, a similar event was organized with the aim of raising capacity in metabarcoding.

ICETA, University of Porto - EnvMetagen Project (EnvMetaGen, Capacity Building at InBIO for Research and Innovation Using Environmental Metagenomics, is an ERA Chair project funded by the European Commission (Grant #668981)