EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists

Date:

 Monday 17 - Friday 21 March 2014

Venue: 

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

Application opens: 

Thursday 01 August 2013

Application deadline: 

Friday 17 January 2014

Participation: 

Open application with selection

Contact: 

Frank O’Donnell

Registration fee: 

£200

Registration closed

Overview

This course will provide an overview of key issues that affect metabolomics studies, bioinformatics tools, and procedures for the analysis of metabolomics data. 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.

Audience

This course is aimed at PhD students and researchers with a minimum of one year’ s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis. Participants must have experience using R (including a basic understanding of the syntax and ability to manipulate objects) and the UNIX/LINUX operating system.

Syllabus, tools and resources

During this course you will learn about…

  • Metabolomics study design, workflow and sources of experimental error
  • Metabolomics data processing: R, XCMS, MetFrag, NMR tools, …
  • Metabolomics data analysis: R, Bioconductor, data fusion, univariate and multivariate data analysis, data clustering and correlation methods…
  • Metabolomics downstream analyses: MetExplore, Cytoscape plugin, metabolic pathway analysis, visualisation, differential expression, metabolomics flux.
  • Metabolomics standards and databases: data dissemination and deposition in EBI-MetaboLights, ISATools and COSMOS

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

Additional information

AllBio sponsored travel bursaries are available for applicants currently working in EU based institutions on research that is non-human / non-medical in nature. Please fill the relevant boxes within the application if you wish to be considered for a travel bursary.

For scientists based in Singapore additional travel grants are available. Please see the website for more information: http://www.a-star.edu.sg/Research/Funding-Opportunities/Grants-Sponsorship/EMBO-Singapore-Cooperation-Agreement.aspx

Programme

Time Topic Trainer
Day 1 – 17 March 2014  Chair: Laura Emery
 13:00 Registration and welcome  
 13:15 Introduction and expectations activity Participants / Laura Emery
 14:30 Participants flash presentations Reza Salek
 15:00 Coffee break  
 15:30 Group activity and discussions: Work flow and experimental design activity All Participants
17:00 Metabolomics: from experimental design to data analysis – Focus on experimental design Oscar Yanes
 17:45 Discussion All Participants
 18:00 Dissecting an untargeted metabolomic workflow Oscar Yanes
 19:00 End  
 19:30 Dinner  
 Day 2 – 18 March 2014  Chair : Reza Salek
 09:15 Overview of the day and MetaboLights Introduction Kenneth Haug
 09:45 Analysis of LCMS-based metabolomics data: feature detection, grouping, quality control, high-throughput analysis, annotation Pietro Francheschi 
 11:00 Tea / coffee break  
 11:30 Analysis of LCMS-based metabolomics data: feature detection, grouping, quality control, high-throughput analysis, annotation Pietro Francheschi  
 13:00 Lunch   
 14:00 The whole story in real-time: data processing and metabolite identification  Steffen Neumann 
 15:30 Tea / coffee break   
 16:00 The whole story in real-time: data processing and metabolite identification  Steffen Neumann 
 17:30 Group activity and discussion  Speakers of day 
 18:30 Poster session  
 19:30 Dinner   
 Day 3 – 19 March 2014 Chair : Reza Salek
09:30 Overview of day Reza Salek 
09:45 "Simple" statistics  Ron Wehrens 
11:00 Break Coffee and discussion   
11:30 Multivariate statistics - only the brave...  Ron Wehrens 
13:00 Lunch   
14:00 Group activity - energizer  Laura Emery and Reza Salek 
14:15 Metabolomics data analysis in the context of metabolic networks  Fabien Jourdan 
15:30 Tea / coffee break   
16:00 Metabolomics data analysis in the context of metabolic networks  Fabien Jourdan 
16:45 Special lecture: Pharmacometabonomics The ability to use pre-dose metabolite profiles data to predict drug responses Jeremy Everett
17:45 Group activity discussion + Selected Participant presentation Speakers of day
19:30 Dinner  
 Day 4 – 20 March 2014 Chair : Reza Salek
 09:30 Overview of day  Reza Salek 
 09:45 Data Fusion – Part 1  Age Smilde 
 10:30 Tea / coffee break   
 11:00 Data Fusion – Part 2 Age Smilde 
 11:30 Discussion and Present your fusion Problem  Selected participants presentation 
 13:00 Lunch   
 14:00 Dealing with sparse matrices in high dimensional metabolomic biomarker applications  Michael Eiden 
 15:30 Tea / coffee break    
 16:00 NMR Workflow data processing to metabolite ID  Reza Salek and Gwenaelle Le Gall 
 18:00 Special workshop KNIME: Visual Programming for Metabolomics (optional) Stephan Beisken
 19:00 Bus to collect from the Wellcome Trust Conference Centre for the course dinner @ Jesus College. Return - 10.30pm.  
 Day 5 – 21 March 2014 Chair : Christoph Steinbeck
 09:30 Overview of day Reza Salek 
 09:45 Metabolomics flux and genome scale  Marta Cascante and Igor Marin De Mas
 11:00 Tea / coffee break   
 11:30 Metabolomics flux and genome scale Marta Cascante and Igor Marin De Mas
 13:00 Lunch  
 13:45 Metabolomics standards: Where are we now? Christoph Steinbeck
 14:15 MetaboLights and data submission Kenneth Haug/Reza Salek
 15:30 Course wrap-up, Q+A and course feedback  All speakers
 16:30 Course end  
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.

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In association with

How to apply

Registration now closed.

Application deadline

17 January 2014

Number of places

30 places

Registration closed

Organisers

Reza Salek - EMBL-EBI, UK

Laura Emery

Christoph Steinbeck - Friedrich-Schiller-University, Jena, Germany

Trainers

Jeremy Everett - University of Greenwich, United Kingdom

Steffen Neumann - Leibniz Institute of Plant Biochemistry

Marta Cascante - University of Barcelona

Igor Marin de Mas - Danmarks Tekniske Universitet

Reza Salek - EMBL-EBI, UK

Oscar Yanes - University Rovira i Virgili (Spain)

Laura Emery - EMBL-EBI, UK

Kenneth Haug - EMBL-EBI, UK

Pietro Franceschi - Fondazione Edmund Mach

Ron Wehrens - Research and Innovation Centre

Fabien Jourdan - INRA France

Age Smilde - University of Amsterdam (Netherlands)

Michael Eiden - Medical Research Council- Human Nutrition Research

Gwenaelle Le Gall - Institute of Food Research

Steffen Neumann - Leibniz Institute of Plant Biochemistry

Christoph Steinbeck - EMBL-EBI, UK

Materials & attachments

EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists