Metabolomics: from data to publication

Date 12 - 15 June 2017
Speaker(s) SIB: Alan Bridge, Mark Ibberson
Fees *academic: 200 CHF   -   for-profit: 0 CHF
Cancellation deadline 1 Jun 2017
City Lausanne
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.

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

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 Of magnets, mice and men: NMR-based metabolomics for biomarker investigation in health and disease Silke Heinzmann
11h45 - 12h30 In Situ Metabolomics by Mass Spectrometry Imaging Aurélien Thomas
12h30 - 14h Lunch
14h - 14h45 Metabolomics-led system’s wide clinical study towards understanding the mechanism of Alzheimer disease Julijana Ivanisevic
14h45 - 15h30 From metabolomics to testable hypotheses Nicola Zamboni
15h30 - 16h Coffee break
16h - 16h45 Network-driven analysis of metabolomics data Nicola Zamboni
16h45 - 17h30 Lipid signatures in diabetes Mark Ibberson