EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists
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Date:
Sunday 14 - Friday 19 February 2016Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Monday 03 August 2015Application deadline:
Friday 13 November 2015Participation:
Open application with selectionContact:
Maria Bacadare GoitiaRegistration fee:
£300 (Includes 6 days accommodation & food)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.
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 - Sunday 14th February | ||
15:30 - 16:00 | Arrival and registration | |
16:00 - 16:15 | Welcome and orientation | Tom Hancocks |
16:15 - 17:45 | Participant flash presentation | All PArticipants |
17:45 - 19:45 | Main poster session with drinks and nibbles | All Participants |
20:00 | Dinner | |
Day 2 - Monday 15th February | ||
08:45- 09:00 | Arrival | |
09:15 - 09:30 | Overview of the day and Introduction | Reza Salek |
09:30 - 10:30 | Metabolomics: from experimental design to data analysis | Oscar Yanes |
10:30 - 11:00 | Tea/coffee break | |
11:00 - 12:30 | Dissecting the multidisciplinary nature of an untargeted metabolomics workflow | Oscar Yanes |
12:30 - 13:30 | Lunch | |
13:30 - 15:30 | Workflow and experimental design group activity | Reza Salek / Oscar Yanes |
15:30 - 16:00 | Metabolomics standard: Where are we now? | Christoph Steinbeck |
16:00 - 16:30 | Tea/coffee break | |
16:30 - 18:00 | Metabolomics resources | David Wishart |
18:00 - 19:30 | Group Discussion | |
19:30 | Evening meal in Hinxton Hall Restaurant | |
Day 3 - Tuesday 16th February | ||
08:45 - 09:00 | Arrival | |
09:15 - 09:30 | Overview of the day and Introduction | Reza Salek |
09:30 - 11:00 | Analysis of LC-MS-based metabolomics data: feature detection, grouping, quality control, high-throughput analysis, annotation | Pietro Francheschi |
11:00 - 11:30 | Tea/coffee break | |
11:30 - 12:30 | Analysis of LC-MS-based metabolomics data: feature detection, grouping, quality control, high-throughput analysis, annotation | Pietro Francheschi |
12:30 - 13:30 | Lunch and Poster session 2 | |
13:30 - 15:00 | Ranking and Data filtering 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 | Tea/coffee break | |
16:30 - 18:30 | The whole story in real-time: data processing and metabolite identification | Steffen Neumann |
18:30 - 19:30 | Discussion in groups: LC-MS missing data and metabolite identification challenges | All Participants |
19:30 | DEvening meal at Hinxton Hall | |
Day 4 - Wednesday 17th February | ||
08:45 - 09:00 | Arrival | |
09:00 - 09:15 | Overview of the day | Reza Salek |
09:15 - 10:30 | GC-MS data analysis workflow and hands-on in metabolomics | Raphael Aggio |
10:30 - 11:00 | Tea/coffee break | |
11:00 - 12:30 | GC-MS data analysis workflow and hands-on in metabolomics | Raphael Aggio |
12:30 - 14:00 | Lunch, Campus tour | |
14:00 - 15:30 | NMR workflow from data processing to metabolite identification | Reza Salek on behalf of Gwenaelle Le Gall |
15:30 - 16:00 | Tea/coffee break | |
16:00 - 17:30 | NMR-based metabolomics data processing and identification using open-source tools | Maria Vinaixa |
17:30 - 18:45 | MetaboLights and data submission | Kalai Vanii Jayaseelan / Reza Salek |
19:30 | Evening meal at Hinxto Hall Restaurant | |
Day 5 - Thursday 18th February | ||
08:45 - 09:00 | Arrival | |
09:00 - 09:15 | Overview of the day | Reza Salek |
09:15 - 10:30 | "Simple" statistics | Ron Wehrens |
10:30 - 11:00 | Tea/coffee break and discussion | |
11:00 - 12:30 | Multivariate statistics - only the brave... | Ron Wehrens |
12:30 - 13:30 | Lunch | |
13:30 - 15:30 | Data Fusion - Part 1 | Johan Westerhuis |
15:30 - 16:00 | Tea/coffee break | |
16:00 - 17:30 | Fusion problem presentations and discussion | All participants |
17:30 - 18:20 | Using Galaxy workflows for metabolomics (http://workflow4metabolomics.org/) | Etienne Thévenot |
18:45 | Depart conference centre for course dinner at Cambridge College | |
19:30 | College dinner | |
22:00 | Bus to return to the Genome Campus | |
Day 6 - Friday 19th February | ||
08:45 - 09:00 | Arrival | |
09:00 - 09:15 | Overview of the day | Reza Salek |
09:15 - 11:00 | Metabolomics flux introduction | Marta Cascante / Igor Marin De Mas |
11:00 - 11:30 | Tea/Coffee break | |
11:30 - 13:00 | Metabolomics flux and genome scale | Marta Cascante / Igor Marin De Mas |
13:00 - 14:00 | Lunch | |
14:00 - 15:15 | Metabolomics data analysis in the context of metabolic networks | Fabien Jordan |
15:15 - 16:00 | Course comments/feedback and Q+A - what we have not covered | |
16:00 | Departures and bus to Cambridge station |