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EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists

14th February 2016 @ 4:00 pm - 19th February 2016 @ 4:00 pm

Reza Salek , EMBL-EBI & Cambridge University, UK
Laura Emery , EMBL-EBI, UK
Christoph Steinbeck , EMBL-EBI, UK
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Registration Opens Date:

Monday, August 3, 2015

Registration Deadline:

Monday, November 2, 2015


Open application with selection


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.

We will have lively and interactive discussion throughout the course in addition to the hands-on data analysis and processing. We encourage you to bring your data, problems you might have with a particular data set or study for group discussion.  You will be asked to present your work and participate in the discussions from day one.



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 Objectives

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


14th February 2016 @ 4:00 pm
19th February 2016 @ 4:00 pm
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Room Kendrew Lecture, The European Bioinformatics Institute
Wellcome Trust Genome Campus
Saffron Walden, CB10 1SD United Kingdom
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