EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists

Date:

 Monday 5 Friday 9 February 2018

Venue: 

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

Application opens: 

Friday August 04 2017

Application deadline: 

Friday November 03 2017

Participation: 

Open application with selection

Contact: 

Emily Rees

Registration fee: 

£350 including accommodation & food

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 to two years of 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, data clustering and regression methods
  • Metabolomics downstream analyses: KEGG, BioCyc, and MetExplore 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; PHENOMenal, workflows4metabolomics
  • Metabolomics Flux and Stable Isotope Resolved Metabolomics (SIRM)

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

We invite participants to bring along a poster to display for the duration of the course. These will serve to facilitate discussion about your research and to convey your reasons for attending the course to others. Posters must be A2 portrait (420mm x 594mm).

Programme

Time Topic Trainer
Day 1 - 5 February 2018
10:00 - 10:30 Arrival and registration  
10:30 - 11:00 Welcome and introduction to EMBL-EBL Tom Hancocks
11:00 - 12:00 Networking and introductions All
12:00 - 13:00 Metabolomics: From experimental design to data analysis Oscar Yanes
13:00 - 14:00 Lunch and posters  
14:00 - 15:30 Dissecting the multidisciplinary nature of an untargeted metabolomics workflow Oscar Yanes
15:30 - 16:00 Break  
16:00 - 16:30 Workflow and experimental design activity All
16:30 - 17:30 Activity group presentations All
17:30 - 18:00 Metabolomics standards – where are we now? Reza Salek
18:00 - 19:00 Welcome drinks and posters All
19:00 - 20:00 Free time  
20:00 Evening meal at Hinxton Hall Resturant  
Day 2 - 6 February 2018
09:00 - 09:05 Overview of day   
09:05 - 10:30 NMR workflow from data processing to metabolite identification Naomi Rankin
10:30 - 11:00 Break   
11:00 - 12:00 NMR-based metabolomics data processing and identification using open-source tools Maria Vinaixa
12:00 - 13:00 Lunch and posters   
13:00 - 14:30 DIMS direct infusion mass spectrometry polar/non-polar Ralf Weber
14:30 - 16:00 DIMS practical - Ralf Ralf Weber
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 Resturant  
Day 3 - 7 February 2018
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 posters   
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 - 19:30 Discussion in Hinxton Hall Bar  
19:30 Evening meal at Hinxton Hall Resturant  
Day 4 - 8 February 2018
09:00 - 09:05 Overview of day  
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 Guided walk in Cambridge  
19:30 - 20:00 Drinks reception at Cambridge College  
20:00 - 22:00 Evening meal at Cambridge College  
22:15 Coach to Wellcome Genome Campus  
Day 5 - 9 February 2018
09:00 - 09:05 Overview of day  
09:05 - 10:00 Deciphering metabolism using Stable Isotope Resolved Metabolomics (SIRM) using GC-MS Silvia Marin
10:00 - 10:30 Break  
10:30 - 12:45 Metabolomics flux introduction and hands on Marta Cascante & Igor Marin De Mas
12:45 - 13:30 Lunch  
13:30 - 14:00 MetaboLights - World-wide data deposition and sharing enables re-analysis and new discoveries Christoph Steinbeck
14:00 - 15:30 MetaboLights and data submission hands on Ken Haug & 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