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 August 01 2013

Application deadline: 

Friday January 17 2014

Participation: 

Open application with selection

Contact: 

Frank O’Donnell

Registration fee: 

£200

Registration closed

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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