Metabolomics Workflows
The application system requires cookies, and the limited processing of your personal data in order to function. By applying to this course you are agreeing to this as outlined in our Privacy Notice and Terms of Use
Date:
Monday 30 October - Thursday 2 November 2017Venue:
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Monday 05 June 2017Application deadline:
Friday 18 August 2017Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£500Registration closed
Overview
This course will provide an introduction to metabolomics data analysis using publicly available software and tools. Participants will become familiar with the current state of data sharing and data standards in metabolomics, particularly through using the EMBL-EBI’s MetaboLights repository. In addition, participants will have a hands-on session using the PhenoMeNal Compute infrastructure. There will be a large practical component, where participants will learn throughhands-on tutorials on data submission, and using a workflow-based approach and compute infrastructure for data analysis, under the guidance of the lecturers and teaching assistants
Audience
This course is aimed at researchers who wish to learn new techniques in metabolomics data analysis using open-source software packages. Familiarity with metabolomics technology such as data acquisition for non-targeted LC-MS is required. Ideally, you should have already started metabolomic data analysis.
Syllabus, tools and resources
-
OpenMS workflows
-
Knime workflows
-
PhenoMeNal
- MetaboLights
Outcomes
After this course you should be able to:
-
Use open source software and web-based tools to construct metabolomics analysis workflows
-
Access metabolomics databases
- Discuss the issues of data sharing and data standards in metabolomics
Programme
Time | Topic | Trainer |
---|---|---|
Day 1 - Monday 30th October 2017 | ||
09:30 - 10:00 | Registration and tea/coffee | |
10:00 - 10:30 | Welcome and introduction | Alexandra Holinski |
10:30 - 11:00 | Overview - your expectations about this course | All instructors |
11:00 - 11:30 | Tea/coffee break | |
11:30 - 13:00 | Overview of Metabolomics data analysis and Workflows (lecture) | Reza Salek and Oliver Kohlbacher |
13:00 - 14:00 | Lunch | |
14:00 - 15:30 | Introduction to OpenMS and KNIME (lecture) | Oliver Kohlbacher |
15:30 - 16:00 | Tea/coffee break | |
16:00 - 17:00 | Preparation for data analysis and visualization using OpenMS (hands-on) | Timo Sachsenberg, Julianus Pfeuffer and Marc Rurik |
17:00 - 18:30 | Discussion and questions | Reza Salek |
19:00 | Evening meal @ Wellcome Trust Conference Centre | |
Day 2 - Tue 31st October 2017 | ||
09:30 - 10:15 | Basics of non-targeted metabolomics data analysis (lecture) | Oliver Kohlbacher |
10:15 - 11:00 | Basics of non-targeted metabolomics data analysis (hands-on) | Timo Sachsenberg, Julianus Pfeuffer and Marc Rurik |
11:00 - 11:30 | Tea/coffee break | |
11:30 - 13:00 | Metabolomics Workflow data analysis Part I (lecture) | Oliver Kohlbacher |
13:00 - 14:00 | Lunch | |
14:00 - 15:30 | Metabolomics Workflow data analysis Part II (hands-on) | Timo Sachsenberg, Julianus Pfeuffer and Marc Rurik |
15:30 - 16:00 | Tea/coffee break | |
16:00 - 17:30 | Downstream data analysis and reporting (hands-on) | Timo Sachsenberg, Julianus Pfeuffer and Marc Rurik |
17:30 - 18:30 | Discussion and questions | Reza Salek |
19:00 | Evening meal @ Wellcome Trust Conference Centre | |
Day 3 - Wednesday 1st November 2017 | ||
09:30 - 10:30 | Metabolite Identification (Camera/MetFrag lecture) | Steffen Neumann |
11:00 - 11:30 | Tea/coffee break | |
11:00 - 13:00 | Metabolite Identification (demo/hand-on using MassBank/MetFrag on PhenoMeNal infrastructure) | René Meier |
13:00 - 14:00 | Lunch | |
14:00 - 14:45 | Metabolomics Standards: where are we now? | Reza Salek |
14:45 - 15:30 | MetaboLights and data sharing - Overview | Reza Salek, Kenneth Haug and Keeva Cochrane |
15:30 - 16:00 | Tea/coffee break | |
16:00 - 18:30 | MetaboLights and data sharing (hands-on) | Reza Salek, Kenneth Haug and Keeva Cochrane |
19:00 | Evening meal @ TBC | |
Day 4 - Thursday 2nd November 2017 | ||
09:30 - 10:00 | Introduction to PhenoMeNal infrastructure | Steffen Neumann and Pablo Moreno |
10:00 - 11:00 | Hands on exploring PhenoMeNal I | Steffen Neumann |
11:00 - 11:30 | Tea/coffee break | |
11:30 - 13:00 | Hands on exploring PhenoMeNal II | Pablo Moreno |
13:00 - 13:30 | Course feedback and informal Q&A | Alexandra Holinski |
13:30 - 14:00 | Lunch and departure |