EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists
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Date:
Monday 5 - Friday 9 February 2018Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Friday 04 August 2017Application deadline:
Friday 03 November 2017Participation:
Open application with selectionContact:
Emily ReesRegistration fee:
£350 including accommodation & foodRegistration 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 to two years of 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, data clustering and regression methods
- Metabolomics downstream analyses: KEGG, BioCyc, and MetExplore 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; PHENOMenal, workflows4metabolomics
- Metabolomics Flux and Stable Isotope Resolved Metabolomics (SIRM)
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
We invite participants to bring along a poster to display for the duration of the course. These will serve to facilitate discussion about your research and to convey your reasons for attending the course to others. Posters must be A2 portrait (420mm x 594mm).
Programme
Time | Topic | Trainer |
---|---|---|
Day 1 - 5 February 2018 | ||
10:00 - 10:30 | Arrival and registration | |
10:30 - 11:00 | Welcome and introduction to EMBL-EBL | Tom Hancocks |
11:00 - 12:00 | Networking and introductions | All |
12:00 - 13:00 | Metabolomics: From experimental design to data analysis | Oscar Yanes |
13:00 - 14:00 | Lunch and posters | |
14:00 - 15:30 | Dissecting the multidisciplinary nature of an untargeted metabolomics workflow | Oscar Yanes |
15:30 - 16:00 | Break | |
16:00 - 16:30 | Workflow and experimental design activity | All |
16:30 - 17:30 | Group presentations | All |
17:30 - 18:00 | Discussion | Reza Salek |
18:00 - 19:00 | Welcome drinks and posters | All |
19:00 - 20:00 | Free time | |
20:00 | Evening meal at Hinxton Hall Resturant | |
Day 2 - 6 February 2018 | ||
09:00 - 09:05 | Overview of day | |
09:05 - 10:30 | NMR workflow from data processing to metabolite identification | Naomi Rankin |
10:30 - 11:00 | Break | |
11:00 - 12:00 | Computer-assisted structure elucidation | Christoph Steinbeck |
12:00 - 13:00 |
Lunch and posters | |
13:00 - 14:00 | Computer-assisted structure elucidation | Christoph Steinbeck |
14:00 - 16:00 | DIMS direct infusion mass spectrometry polar/no-polar | Ralf Weber |
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 Resturant | |
Day 3 - 7 February 2018 | ||
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 posters | |
13:30 - 15:00 | Exploring LC-MS data matrix: missing values, visualisation and data filtering | Samantha Riccadonna |
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 - 19:30 | Discussion in Hinxton Hall Bar | |
19:30 | Evening meal at Hinxton Hall Resturant | |
Day 4 - 8 February 2018 | ||
09:00 - 09:05 | Overview of day | |
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 | MetaboLights and data submission |
Keeva Cochrane & Ken Haug |
18:15 | Coach to Cambridge | |
18:45 - 19:30 | Free time in Cambridge | |
19:30 - 20:00 | Drinks reception at Cambridge College | |
20:00 - 22:00 | Evening meal at Cambridge College | |
22:15 | Coach to Wellcome Genome Campus | |
Day 5 - 9 February 2018 | ||
09:00 - 09:05 | Overview of day | |
09:05 - 10:00 | Deciphering metabolism using Stable Isotope Resolved Metabolomics (SIRM) using GC-MS | Silvia Marin |
10:00 - 10:30 | Break | |
10:30 - 12:45 | Metabolomics flux | Marta Cascante & Igor Marin De Mas |
12:45 - 13:30 | Lunch | |
13:30 - 14:00 | Metabolomics standards | Reza Salek |
14:00 - 15:30 | Metabolomics data analysis in Cloud using PheNoMeNal Pablo Moreno | Pablo Moreno |
15:30 - 15:45 | Course feedback and wrap up | Tom Hancocks |
15:45 | End of course | |
16:00 | Coach to Cambridge Railway Station |