EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists
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Date:
Monday 13 - Friday 17 February 2017Venue:
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Monday 08 August 2016Application deadline:
Wednesday 16 November 2016Participation:
Open application with selectionContact:
Maria Bacadare GoitiaRegistration fee:
£350Registration closed
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 |