EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists


 Sunday 14 -Friday 19 February 2016


European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday August 03 2015

Application deadline: 

Monday November 02 2015


Open application with selection

Registration fee: 

£300 (Includes 6 days accommodation & food)

Course overview

This course will provide an overview of key issues that affect metabolomics studies, handling dataset and procedures for the analysis of metabolomics data using bioinformatics tools. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field of metabolomics, from study design to metabolite identification.


This course is aimed at PhD students, post-docs and researchers with at least one year’s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis. Participants ideally must have working experience using R (including a basic understanding of the syntax and ability to manipulate objects).

Syllabus, tools and resources

During this course you will learn about:

  • Metabolomics study design, workflows and sources of experimental error, difference between target and un-target approaches.
  • Metabolomics data processing tools: hands on open source R based programs, XCMS, MetFrag, MetFusion, rNMR, BATMAN
  • Metabolomics data analysis: Using R Bioconductor, understanding usage of univariate and multivariate data analysis, data fusion concepts and data clustering
  • Metabolomics downstream analyses: KEGG, BioCyc, MetExplore and Cytoscape for metabolic pathway and network analysis with visualisation of differential expression, understanding metabolomics flux analysis.
  • Metabolomics standards and databases: data dissemination and deposition in EMBL- EBI MetaboLights repository, collection and ever growing metabolomics online resource, COSMOS data standards, MSI

Learning outcomes

After this course you should be able to:

  • Discuss major principles of metabolomics experimental design and factors that impact upon subsequent analysis
  • Identify strengths and weaknesses in a variety of metabolomics analytical approaches
  • Use a range of Bioinformatics software to pre-process, process and analyse metabolomics data
  • Discuss current trends and challenges in metabolomics 


Time Topic Trainer
Day 1 - Sunday 14th February
16:00 - 16:15 Registration and welcome 
16:15 - 17:30 Workshop overview and group activity Laura Emery
17:30 - 18:00 Participant flash presentation  Reza Salek 
18:00 - 19:00 Main poster session with drinks and nibbles All Partcipants 
20:00 Dinner 
Day 2 - Monday 15th February
09:15 - 09:30 Overview of the day and Introduction  Reza Salek
09:30 - 10:30 Metabolomics: from experimental design to data analysis Oscar Yanes  
10:30 - 11:00 Tea/coffee break 
11:00 - 12:30 Dissecting the multidisciplinary nature of an untargeted metabolomics workflow Oscar Yanes 
12:30 - 13:30 Lunch 
13:30 - 15:30 Workflow and experimental design group activiy All Participants 
15:30 - 16:00 Metabolomics standard: Where are we now? Christoph Steinbeck
16:00 - 16:30 Tea/coffee break 
16:30 - 18:00 Metabolomics resources  David Wishart
18:00 - 19:30 Group Discussion  
19:30  Dinner 
Day 3 - Tuesday 16th February
09:15 - 09:30 Overview of the day and Introduction Reza Salek 
09:30 - 11:00 Analysis of LC-MS-based metabolomics data: feature detection, grouping, quality control, high-throughput analysis, annotation Pietro Francheschi 
11:00 - 11:30 Tea/coffee break 
11:30 - 12:30 Analysis of LC-MS-based metabolomics data: feature detection, grouping, quality control, high-throughput analysis, annotation Pietro Francheschi 
12:30 - 13:30 Lunch and Poster session 2 
13:30 - 15:00 Ranking and Data filtering metabolic features to identified metabolites Maria Vinaixa 
15:00 - 16:00 The whole story in real-time: data processing and metabolite identification Steffen Neumann
16:00 - 16:30 Tea/coffee break  
16:30 - 18:30 The whole story in real-time: data processing and metabolite identification Steffen Neuman 
18:30 - 19:30 Group activity LC-MS missing data and metabolite identification challenges discussion  
19:30 Dinner  
Day 4 - Wednesday 17th February 
09:30 - 09:45 Overview of the day Reza Salek
09:45 - 11:00 NMR workflow from data processing to metabolite identification Gwenaelle Le Gall 
11:00 - 11:30 Tea/coffee break 
11:30 - 12:45 NMR-based metabolomics data processing and identification using open-source tools Maria Vinaixa
12:45 - 13:15 Lunch 
13:15 - 14:15 Group activity – brisk walk around campus  
14:15 - 15:30  GC-MS data analysis workflow and hands-on in metabolomics Raphael Aggio
15:30 - 16:00 Tea/coffee break 
16:00 - 17:30 GC-MS data analysis workflow and hands-on in metabolomics Raphael Aggio 
17:30 - 18:45 MetaboLights and data submission Ken Haug / Reza Salek
18:45 - 19:30 NMR and GC-MS Group activity / selected participant presentations  
19:30 Dinner
Day 5 - Thursday 18th February
09:30 - 09:45 Overview of the day Reza Salek 
09:45 - 11:00 "Simple" statistics        Ron Wehrens
11:00 - 11:30 Tea/coffee break and discussion 
11:30 - 13:00 Multivariate statistics - only the brave... Ron Wehrens 
13:00 - 14:00 Lunch 
14:00 - 15:00 Data Fusion - Part 1 Age Smilde
15:00 - 15:30 Tea/coffee break 
15:30 - 16:30 Data Fusion - Part 2 Age Smilde 
16:30 - 17:45 Discussion and present your fusion problem Selected participant presentations
17:45 - 18:45 Group activity discussion on Stats / selected participant presentations  
18:45 Depart conference centre for course dinner at Cambridge College 
19:30 College dinner  
22:00 Bus to return to the Genome Campus  
Day 6 - Friday 19th February
09:15 - 09:30  Overview of the day   
09:30 - 11:00 Metabolomics data analysis in the context of metabolic networks Fabien Jordam
11:00 - 11:30 Tea/Coffee break
11:30 - 13:00 Metabolomics flux introduction Marta Cascante / Igor Marin De Mas
13:00 - 14:00 Lunch
14:00 - 15:15 Metabolomics flux and genome scale Marta Cascante / Igor Marin De Mas
15:15 - 16:00 Course comments and Q+A - what we have not covered   
16:00 Departures and bus to Cambridge station  
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

At EMBL-EBI, we manage the world’s public biological data and make it freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. Set on the beautiful Wellcome Genome Campus near Cambridge in the UK, we support scientists throughout the world in seeking solutions to challenges in healthcare, agriculture and the environment.


In association with

How to apply

In order to be considered for a place on this course applicants must do the following:

  1. Complete the online application form.
  2. Submit a PDF document to eventmgt@ebi.ac.uk containing a short biography including your work history and a description of your current research interests. Each document should be no longer than 150 words.
  3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course.

Further details will be provided on your confirmation email after completing the online form.

Incomplete applications will NOT be considered. Please read through the following guidance document for more information on how to complete your application.

Application deadline

02 November 2015

Number of places

30 places


David Wishart - University of Alberta, Edmonton, Canada

Raphael Aggio - School of Biological Sciences - University of Auckland, Australia

Christoph Steinbeck - EMBL-EBI, UK

Reza Salek - EMBL-EBI, UK

Laura Emery - EMBL-EBI, UK

Oscar Yanes - University Rovira i Virgili (Spain)

Pietro Franceschi - Research and Innovation Centre

Maria Vinaixa - Rovira i Virgili University

Steffen Neumann - Leibniz Institute of Plant Biochemistry

Gwenaelle Le Gall - Institute of Food Research

Kenneth Haug - EMBL-EBI, UK

Ron Wehrens - Research and Innovation Centre

Age Smilde - University of Amsterdam (Netherlands)

Fabien Jourdan - INRA France

Marta Cascante - University of Barcelona

Igor Marin De Mas - Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences