EMBL-EBI Workshop: Data and tools for transcriptomics and protein biology


 Tuesday 31 July Wednesday 1 August 2018


University of Malta - Faculty of ICT Room TR03,  Msida,  MDS2080,  Malta

Application opens: 

Wednesday 30 May 2018

Application deadline: 

Monday 09 July 2018


Open application with selection


Joseph Borg

Registration fee: 


Registration closed

Find other similar courses »

Course Overview

In this course participants will explore EMBL-EBI resources for transcriptomics and protein biology applications. The sessions focus on browsing, searching and retrieving both functional genomics and protein sequence data, as well as how to classify and predict the function of novel sequences.


This course is aimed at wet-lab and clinical researchers at any career stage within the University of Malta who are working with and/or generating their own transcriptomic and protein sequence datasets. No computational or previous bioinformatics experience is required for this workshop, but an undergraduate level knowledge of biology or biochemistry would be an advantage.


  • introduction-embl-ebi-resources-and-tools
  • arrayexpress-public-database-functional-genomics
  • expression-atlas-gene-expression-across-species-and-biological-conditions
  • protein-sequence-databases
  • functional-protein-classification-interpro

Learning outcomes

After this course participants should be able to:

  • Identify and use a variety of EMBL-EBI tools to access, retrieve and export data from resources relevant to individual areas of interest.
  • Browse, search and retrieve functional genomics data from ArrayExpress
  • Find information on the abundance and localisation of RNA (and proteins) in different species and biological conditions.
  • Explore gene co-expression and perform gene set overlap analysis.
  • Identify information about all aspects of a protein of interest such as function, interactions and disease association, as well as investigate protein homology through similarity searches and alignments.
  • Use the InterPro database to classify protein sequences based on underlying protein family models, interpret InterPro annotations, and summarize the application of InterPro data to annotate large-scale sequence datasets.


Day 1 – Tuesday 31 July 2018
09:00-09:30 Welcome and introduction to EMBL-EBI resources and tools Laura Huerta
09:30-10.30 Data quality: standards and ontologies Laura Huerta
10:30-11:00 Break
11:00-12:00 Discover functional genomics data with ArrayExpress Laura Huerta
12:00-13:00 Lunch
13:00-14:00 Discover functional genomics data with ArrayExpress: Practical session Laura Huerta
14:00-15:00 Explore gene expression data with Expression Atlas Laura Huerta
15:00-15:30 Break  
15:30-16:30 Explore gene expression data with Expression Atlas: Practical session Laura Huerta
16:30-17:30 Single Cell Expression Atlas: a new tool for single cell transcriptomics Laura Huerta
17:30 End of day 1  
Day 2 – Wednesday 1 August 2018
09:00-10:30 UniProt Rossana Zaru
10:30-11:00 Break
11:00-12:30 UniProt Rossana Zaru
12:30-13:30 Lunch
13:30-15:00 InterPro Lorna Richardson
15:00-15:30 Break  
15:30-17:00 InterPro Lorna Richardson
17:00-17:15 End of day and feedback Lorna Richardson