Metabolomics: from data to publication

Event Start Date 12 Jun 2017
Event End Date 15 Jun 2017
Fee Free for members of the CUSO/StarOmics program. 200 CHF for academics. Others, please contact us
Cancellation deadline 1 June 2017
Application status Open
Location University of Lausanne - Génopode

This course is co-organised by the CUSO/StarOmics doctoral program. Priority is given to its members, but is open to everyone.



We aim at detailing state-of-the-art advancement of metabolomics, which represents a powerful approach and an alternative to the classical other omics. It represents a better phenotypic picture by reflecting the biochemical activity of the cells. This course will provide an overview of handling metabolomics data (from rawdata to biological knowledge) using bioinformatics tools. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions


This course targets phD students, postdocs

Learning objectives

At the end of this course, participants are expected to be able to:

  • pre-process LC-MS metabolomics raw data;
  • process and analyse metabolomics data;
  • understand and discuss current trends and challenges in metabolomics


Knowledge / competencies:

Although not required, basic knowledge of mass spectrometry, analytical chemistry, and statistics is a plus.


Participants must bring a laptop


Application is open, please click on the link at the bottom of the page.

No registration fees for members of staromics, otherwise they are 200 CHF for academics. This includes course content material, coffee breaks and a social dinner. Participants from non-academic institutions should contact us before application.

Deadline for registration and free-of-charge cancellation is set to June 1, 2017. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to this and other general conditions, available here.


University of Lausanne, Génopode Building, room 2020 (UNIL sorge M1 line stop)

Additional information

Coordination: Florence Mehl (SIB/UNIL), Grégoire Rossier (SIB), Corinne Dentan (UNIL/CUSO/Staromics)

You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

For more information, please contact This email address is being protected from spambots. You need JavaScript enabled to view it.

Provisional program

 Monday 12 June

 9h - 10h   Introduction to metabolomics   J-L. Wolfender & S. Rudaz 
 10h - 11h   Metabolomics repository – data access, storage and sharing   Reza Salek 
 11h - 11h30   Coffee break   
 11h30 - 13h   LC-MS data pre-processing with XCMS/CAMERA   Paul Benton 
 13h - 14h   Lunch   
 14h - 15h30   Features filtering   Maria Vinaixa 
 15h30 - 16h   Coffee break   
 16h - 17h30   Multivariate analysis   Julien Boccard 


Tuesday 13 June

 9h - 10h30   Metabolite identification with mass-spectrometry   Maria Vinaixa 
 10h30 - 11h   Coffee break   
 11h - 12h30   METLIN database   Paul Benton 
 12h30 - 14h   Lunch   
 14h - 15h30   Non-target identification with High Resolution Mass Spectrometry: Gathering the Evidence   Emma Schymanski 
 15h30 - 16h   Coffee break   
 16h - 17h30   Knowledge representations and resources for metabolomics   Alan Bridge 


Wednesday 14 June – Workflow4Metabolomics hands-on course

 9h - 10h30   Introduction to Galaxy and Workflow4Metabolomics   Yann Guitton 
 10h30 - 11h   Coffee break   
 11h - 12h30   LC-MS data pre-processing   Yann Guitton 
 12h30 - 14h   Lunch   
 14h - 15h30   MS data processing (filtering and correcting data)   Yann Guitton 
 15h30 - 16h   Coffee break   
 16h - 17h30   Downstream analysis (statistical workflow and metabolite identification)   Yann Guitton 


Thursday 15 June – Workshops (titles to be announced)

 9h – 9h45     Franco Moritz 
 9h45 - 10h30   Generation and annotation of molecular networks   Pierre-Marie Allard 
 10h30 - 11h   Coffee break   
 11h - 11h45     Silke Heinzmann 
 11h45 - 12h30   In Situ Metabolomics by Mass Spectrometry Imaging   Aurélien Thomas 
 12h30 - 14h   Lunch   
 14h - 14h45     Julijana Ivanisevic 
 14h45 - 15h30     Nicola Zamboni 
 15h30 - 16h   Coffee break   
 16h - 16h45     Nicola Zamboni 
 16h45 - 17h30     Mark Ibberson