PhenoMeNal Gateway: Portal to metabolomics data analysis in the cloud


 Wednesday 6 Friday 8 June 2018


Tennis Court Suite, Wellcome Genome Campus - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Wednesday March 07 2018

Application deadline: 

Friday April 27 2018


Open application with selection


Frank O’Donnell

Registration fee: 



This course will provide an introduction to metabolomics data analysis in a cloud computing environment, based on resources developed and provided by the PhenoMeNal project. PhenoMeNal is a comprehensive and standardised e-infrastructure that supports data processing and analysis workflows for data generated by metabolomics studies. Participants will become familiar with a range of relevant open-source tools and workflows developed by PhenoMeNal.  There will be a large practical component, where participants will learn through hands-on tutorials to use a workflow-based approach and compute infrastructure for data analysis and data submission, under the guidance of expert trainers and teaching assistants.


This course is aimed at researchers in metabolomics and bioinformatics who wish to learn new techniques in metabolomics data analysis using the cloud platform. Participants should have some metabolomics experience and an interest in computational data analysis. Some experience in Galaxy will be helpful, but not strictly required.

Syllabus, tools and resources

  • Introduction to PhenoMeNal tools and infrastructure
  • Creating a cloud research environment (e.g running in AWS)
  • Tools and workflows in Galaxy


After this course you should be able to:

  • Set up a PhenoMeNal cloud research environment (CRE)
  • Use Galaxy to create metabolomics analysis workflows
  • Access metabolomics databases
  • Discuss the issues of data sharing and data standards in metabolomics


Time Topic Trainer
Day 1 - 6th June 2018
09:30 - 10:00 Registration and tea/coffee  
10:00 - 11:00 An introduction to PhenoMeNal Pablo Moreno and Noureddin Sadawi
11:00 - 11:30 Tea/coffee break  
11:30 - 13:00 PhenoMeNal Portal; using the public instance and deploying on AWS: Hands-on session Pablo Moreno
13:00 - 14:00 Lunch  
14:00 - 14:30 PhenoMeNal Portal (Continued) Pablo Moreno
14:30 - 15:30 Metabolite profiling using XCMS and CAMERA/MetFrag Steffen Neumann
15:30 - 16:00 Tea/coffee break  
16:00 - 17:30 LC/MS data analysis with XCMS and MetFrag on PhenoMeNal Steffen Neumann and Pablo Moreno
17:30 - 17:40 Break  
17:40 - 18:00 Exercises Namrata Kale
18:00 Dinner, followed by bus back to Cambridge   
Day 2 - 7th June 2018
09:30 - 10:30 Data standards For Metabolomics and FAIR datasets: PhenoMenal Data Management Workflows in Galaxy Phillipe Rocco-Serra
10:30 - 11:00 Introduction to MetaboLights Ken Haug
11:00 - 11:30 Tea/coffee break  
11:30 - 12:00 Fundamentals of fluxomics Pedro de Atauri and Vitaly Selivanov
12:00 - 13:00 Fluxomics workflow: Running an existing workflow Pedro de Atauri and Vitaly Selivanov
13:00 - 14:00 Lunch  
14:00 - 15:00 Fluxomics workflow: Build your workflow Pablo Moreno
15:00 - 15:30 Introduction to statistical analysis Etienne Thevenot
15:30 - 16:00 Tea/coffee break  
16:00 - 17:30 Univariate and multivariate analysis of metabolomics data Etienne Thevenot
17:30 - 17:40 Break  
17:40 -18:00 Exercises Namrata Kale
18:00 Dinner, followed by bus back to Cambridge  
Day 3 - 8th June 2018
09:30 - 10:30 Example of start to end LC/MS workflow using Galaxy Ola Spjut
10:30 - 11:00 Tea/coffee break  
11:00 - 11:30 Example of clinical metabolomics projects using start to end workflows Ola Spjut
11:30 - 12:00 Course feedback and wrap up  
12:00 - 13:00 Lunch and end of workshop