Metabolomics Workflows

Date:

 Monday 30 October Thursday 2 November 2017

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday June 05 2017

Application deadline: 

Friday August 18 2017

Participation: 

Open application with selection

Contact: 

Frank O’Donnell

Registration fee: 

£500

Registration closed

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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