EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists
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Date:
Monday 17 - Friday 21 March 2014Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Thursday 01 August 2013Application deadline:
Friday 17 January 2014Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£200Registration closed
Overview
This course will provide an overview of key issues that affect metabolomics studies, bioinformatics tools, and procedures for the analysis of metabolomics data. 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.
Audience
This course is aimed at PhD students and researchers with a minimum of one year’ s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis. Participants must have experience using R (including a basic understanding of the syntax and ability to manipulate objects) and the UNIX/LINUX operating system.
Syllabus, tools and resources
During this course you will learn about…
- Metabolomics study design, workflow and sources of experimental error
- Metabolomics data processing: R, XCMS, MetFrag, NMR tools, …
- Metabolomics data analysis: R, Bioconductor, data fusion, univariate and multivariate data analysis, data clustering and correlation methods…
- Metabolomics downstream analyses: MetExplore, Cytoscape plugin, metabolic pathway analysis, visualisation, differential expression, metabolomics flux.
- Metabolomics standards and databases: data dissemination and deposition in EBI-MetaboLights, ISATools and COSMOS
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
AllBio sponsored travel bursaries are available for applicants currently working in EU based institutions on research that is non-human / non-medical in nature. Please fill the relevant boxes within the application if you wish to be considered for a travel bursary.
For scientists based in Singapore additional travel grants are available. Please see the website for more information: http://www.a-star.edu.sg/Research/Funding-Opportunities/Grants-Sponsorship/EMBO-Singapore-Cooperation-Agreement.aspx
Programme
Time | Topic | Trainer |
---|---|---|
Day 1 – 17 March 2014 Chair: Laura Emery | ||
13:00 | Registration and welcome | |
13:15 | Introduction and expectations activity | Participants / Laura Emery |
14:30 | Participants flash presentations | Reza Salek |
15:00 | Coffee break | |
15:30 | Group activity and discussions: Work flow and experimental design activity | All Participants |
17:00 | Metabolomics: from experimental design to data analysis – Focus on experimental design | Oscar Yanes |
17:45 | Discussion | All Participants |
18:00 | Dissecting an untargeted metabolomic workflow | Oscar Yanes |
19:00 | End | |
19:30 | Dinner | |
Day 2 – 18 March 2014 Chair : Reza Salek |
||
09:15 | Overview of the day and MetaboLights Introduction | Kenneth Haug |
09:45 | 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 | |
14:00 | The whole story in real-time: data processing and metabolite identification | Steffen Neumann |
15:30 | Tea / coffee break | |
16:00 | The whole story in real-time: data processing and metabolite identification | Steffen Neumann |
17:30 | Group activity and discussion | Speakers of day |
18:30 | Poster session | |
19:30 | Dinner | |
Day 3 – 19 March 2014 Chair : Reza Salek | ||
09:30 | Overview of day | Reza Salek |
09:45 | "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 | Special lecture: Pharmacometabonomics The ability to use pre-dose metabolite profiles data to predict drug responses | Jeremy Everett |
17:45 | Group activity discussion + Selected Participant presentation | Speakers of day |
19:30 | Dinner | |
Day 4 – 20 March 2014 Chair : Reza Salek | ||
09:30 | Overview of day | Reza Salek |
09:45 | Data Fusion – Part 1 | Age Smilde |
10:30 | Tea / coffee break | |
11:00 | Data Fusion – Part 2 | Age Smilde |
11:30 | Discussion and Present your fusion Problem | Selected participants presentation |
13:00 | Lunch | |
14:00 | Dealing with sparse matrices in high dimensional metabolomic biomarker applications | Michael Eiden |
15:30 | Tea / coffee break | |
16:00 | NMR Workflow data processing to metabolite ID | Reza Salek and Gwenaelle Le Gall |
18:00 | Special workshop KNIME: Visual Programming for Metabolomics (optional) | Stephan Beisken |
19:00 | Bus to collect from the Wellcome Trust Conference Centre for the course dinner @ Jesus College. Return - 10.30pm. | |
Day 5 – 21 March 2014 Chair : Christoph Steinbeck | ||
09:30 | Overview of day | Reza Salek |
09:45 | Metabolomics flux and genome scale | Marta Cascante and Igor Marin De Mas |
11:00 | Tea / coffee break | |
11:30 | Metabolomics flux and genome scale | Marta Cascante and 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 | Course wrap-up, Q+A and course feedback | All speakers |
16:30 | Course end |