EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists

Date:

 Monday 16 Friday 20 February 2015

Venue: 

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

Application deadline: 

Monday 15 December 2014

Participation: 

Open application with selection

Registration fee: 

£200

Registration closed

Overview

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.

Audience

This course is aimed at PhD students, post-docs and researchers with at least two or three 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 - 16 Feb 2015 Chair: Laura Emery
13:00 Registration and welcome  
13:15 Introduction and expectations activity Laura Emery
14:30 Participants flash presentations 2.5 min each Reza Salek
15:00 Coffee break  
15:30 Work flow and experimental design group activity Reza Salek
17:00 Metabolomics: from experimental design to data analysis – Focus on experimental design Oscar Yanes
17:45 Discussion and problem solving With Speakers of day
18:00 Dissecting the multidisciplinary nature of an untargeted metabolomics workflow Oscar Yanes
19:00 Networking Session with pre-dinner drinks  
19:30 Dinner  
Day 2 - 17 Feb 2015 Chair: Reza Salek
09:15 Over view of the day  
09:30 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 - Poster session  
14:00 The whole story in real-time: MS data processing and metabolite identification Steffen Neumann
15:30 Tea/coffee break  
16:00 The whole story in real-time: MS data processing and metabolite identification Steffen Neumann
17:30 Tracking metabolic addiction of cancer cells using a systems biology approach George Poulogiannis
18:30 Metabolite identification  - Group activity and discussion with problem solving  
19:30 Dinner  
Day 3 - 18 Feb 2015    Chair: Reza Salek
09:15 Overview of day Reza Salek
09:30 "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 Resources Centre for Stable Isotope Resolved Metabolomics: Tracing Networks & Pools Rick Higashi
17:45 Group activity data analysis discussion + Selected Participant presentation on their datasets Speakers of day
19:30 Dinner  
Day 4 - 19 Feb 2015    Chair: Reza Salek
09:30 Overview of day Reza Salek
09:45 Data Fusion – Part 1 Johan Westerhuis
10:30 Tea / coffee break  
11:00 Data Fusion – Part 2 Johan Westerhuis
11:30 Discussion and Present your fusion Problem Selected participants
13:00 Lunch  
14:00 NMR workflow from data processing to metabolite ID Gwenaelle Le Gall
15:30 Tea / coffee break   
16:00 NMR-based metabolomics data processing and identification using open-source tools Maria Vinaixa
17:45 Group activity discussion + Selected Participant presentation Data session
18:45 Depart conference centre for Course dinner at Cambridge College  
Day 5 - Date - 20 Feb 2015   Chair: Christoph Steinbeck
09:30 Overview of day Reza Salek
09:45 Metabolomics flux introduction Marta Cascante & Igor Marin De Mas
11:00 Tea/coffee break  
11:30 Metabolomics flux and genome scale Marta Cascante & 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 Metabolomics resources - What we have not covered– Q+A Reza Salek
16:45 Course wrap-up and feedback Laura Emery
17:00 Course closing comments and feedback session