EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists
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
Learning Objectives
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
| Time | Topic | Trainer |
|---|---|---|
| Day 1 – 17 March 2014 Chair: Laura Emery | ||
| 13:00 | Registration and welcome | |
| 13:15 | Introduction and group activity | Participants / Laura Emery |
| 14:30 | Participants flash presentations | Reza Salek |
| 15:00 | Coffee break | |
| 15:30 | Metabolomics: from experimental design to data analysis – Focus on experimental design | Oscar Yanes |
| 16:30 | Group Discussion: Working on your experimental design | All Participants |
| 17:15 | Dissecting an untargeted metabolomic workflow | Oscar Yanes |
| 18:15 | Group Discussion: Work flow | All Participants |
| 19:00 | End | |
| 19:30 | Dinner | |
| Day 2 – 18 March 2014 Chair : Kenneth Haug | ||
| 09:30 | Over view 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 | Free time | |
| 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 | Group activity discussion + Selected Participant presentation | Speakers of day |
| 18:30 | Free time | |
| 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 | Free time | |
| 18:45 | Depart conference centre for Course dinner at Cambridge College | |
| Day 5 – 21 March 2014 Chair : Christoph Steinbeck | ||
| 09:30 | Overview of day | Reza Salek |
| 09:45 | Metabolomics flux and genome scale | TBC – Marta Cascante |
| 10:30 | Tea / coffee break | |
| 11:00 | Metabolomics standards: Where are we now? | Christoph Steinbeck |
| 11:45 | MetaboLights and data submission | Kenneth Haug |
| 13:00 | Lunch | |
| 14:00 | Metabolomics Databases | Reza Salek |
| 15:00 | Course wrap-up and Q+A | All speakers |
| 16:00 | Course end | |
Application will be via a selection process therefore applicants should be aware that, in order to be considered for place on this course, they MUST complete the online application page as well as submit a short CV, research interests and a letter of support from their supervisor or another senior co-worker explaining why they should be selected for this course. Incomplete applications will NOT be considered. Details of how to submit these extra documents will be provided on your application confirmation email.
Application registration closes 17 January 2014 (12:00 midday GMT). There will be a maximum of 25 participants on this course. Successful applicants will be notified by 31 January 2014 and will then be asked to confirm their place on the course by re-registering and paying the course fee.
Please note that the registration fee of £100.00 includes:
- All meals listed in the agenda (breakfast, lunch, dinner and refreshment breaks)
- Course materials on a USB
- Use of a computer in the EMBL-EBI IT Training Room throughout the course
- Accommodation at the Holiday Inn Express Duxford for 4 nights (17-21 March 2014)
To apply for this event please use the following link. Items marked * are mandatory. Incomplete applications will not be processed.