EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists

Date:

 Monday 13 Friday 17 February 2017

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday August 08 2016

Application deadline: 

Wednesday November 16 2016

Participation: 

Open application with selection

Registration fee: 

£350

Registration closed

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Overview

This course will provide an overview of key issues that affect metabolomics studies, handling datasets 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.

Audience

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

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

Programme

Time Topic Trainer
Day 1 - Monday 13 February
10:00 - 10:30 Arrival and registration  
10:30 - 11:00 Welcome and introduction to EMBL-EBI Tom Hancocks
11:00 - 12:00 Networking activities All
12:00 - 13:00 Metabolomics: From experimental design to data analysis Oscar Yanes
13:00 - 14:00 Lunch   
14:00 - 15:30 Dissecting the multidisciplinary nature of an untargeted metabolomics workflow Oscar Yanes
15:30 - 16:00 Workflow and experimental design activity  All
16:00 - 16:30 Break  
16:30 - 17:30 Workflow and experimental design activity All
17:30 - 18:00 Metabolomics standards – where are we now? Reza Salek
18:00 - 19:00 Welcome drinks and posters All
19:15 Check in at Conference Centre  
20:00 Evening meal at Hinxton Hall Restaurant  
Day 2 - Tuesday 14 February
08:45 - 09:00 Arrival  
09:00 - 09:05 Overview of day Reza Salek
09:05 - 11:00

Analysis of LC-MS-based metabolomics data

Pietro Francheschi

11:00 - 11:30 Break  
11:30 - 12:30

Analysis of LC-MS-based metabolomics data

Pietro Francheschi 

12:30 - 13:30 Lunch and poster session  
13:30 - 15:00 Ranking and data filtering of 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 Break  
16:30 - 18:30 The whole story in real-time: data processing and metabolite identification

Steffen Neumann

18:30 End of day  
18:30 - 19:30 Discussion in Hinxton Hall Bar  
19:30 Evening meal at Hinxton Hall Restaurant  
Day 3 - Wednesday 15 February
08:45 - 09:00 Arrival  
09:00 - 09:05 Overview of day Reza Salek
09:05 - 10:30 DIMS direct infusion mass spectrometry polar/non-polar

Ralf Weber

10:30 - 11:00 Break  
11:00 - 12:30 DIMS practical Ralf Weber
12:30 - 13:30 Lunch and poster session  
13:30 - 14:00 NMR workflow from data processing to metabolite identification Naomi Rankin
14:00 - 16:00 NMR-based metabolomics data processing and identification using open-source tools Maria Vinaixa
16:00 - 16:30 Break  
16:30 - 18:30 Metabolomics data analysis in the context of metabolic networks

Fabien Jourdan

18:30 - 19:30 Discussion in Hinxton Hall Bar  
19:30 Evening meal at Hinxton Hall Restaurant  
Day 4 - Thursday 16 February
08:45 - 09:00 Arrival  
09:00 - 09:05 Overview of day Reza Salek
09:05 - 10:30 Simple statistics Jos Hageman
10:30 - 11:00 Break  
11:00 - 12:30  Multivariate statistics: only the brave

Jos Hageman

12:30 - 13:30 Lunch and posters  
13:30 - 15:30 Data Fusion  Johan Westerhuis 
15:30 - 16:00 Break  
16:00 - 18:00

Using Galaxy workflows for metabolomics

Etienne Thevenot

18:15 Coach to Cambridge  
18:45 - 19:30 Free time in Cambridge  
20:00 Evening meal at a Cambridge College  
22:00 Coach to Wellcome Genome Campus  
Day 5 - Friday 17 February
08:45 - 09:00 Arrival  
09:00 - 09:05 Overview of day  
09:00 - 10:30

Metabolomics flux introduction

Marta Cascante & Igor Marin De Mas
10:30 - 11:00 Break  
11:00 - 12:30 Metabolomics flux and genome scale Marta Cascante & Igor Marin De Mas
12:30 - 13:30 Lunch and posters  
13:30-13:50 MetaboLights - an open access repository for metabolomics data  Chris Steinbeck
13:50 - 15:30 MetaboLights and data submission Ken Haug, Kalai Jayaseelan, Keeva Cochrane
15:30 - 15:45 Course feedback and wrap up Tom Hancocks
15:45 End of course  
16:00 Coach to Cambridge Railway Station