With the increased production of proteomic data, one of the major challenges lies in our ability to annotate and explore these long lists of proteins for biological interpretation. ProteoRE (Proteomics Research Environment) is a centralized infrastructure available online (http://www.proteore.org) that allows biologists/clinicians with no programming experience to manipulate and interpret their proteomics data in an interactive, reproducible and collaborative manner. Benefiting from the functionalities of the Galaxy environment, ProteoRE allows you to run annotation, functional analysis and graphical visualization tools, build and share complete analysis chains via documented user interfaces. In its current version, ProteoRE allows proteomic data from human, mouse and rat samples to be analyzed.


This course is intended for life scientists who are already dealing with proteomics data or willing to efficiently use publicly available proteomics data, and would like to be able to start analysing them.

Learning objectives

Participants will learn how to use the features of ProteoRE to interpret and manipulate proteomics data based on two real case studies: i. annotation of the proteome of a human biological sample; ii. implementation of a strategy for selecting biomarker candidates. This training also includes presentations on public data sources and functional analysis strategies. At the end of the course, participants should be able to:

  • manipulate their data (filtering, cross-comparison, ID conversion),
  • annotate protein lists,
  • carry out functional analyses (enrichment tests, exploration of biological networks),
  • build a processing chain (“workflow”) for re-run and automation purposes
  • manage and share their results under Galaxy in a collaborative context and for publication purposes (texts, graphics, workflow and history).


No specific prerequisite required


Participants should bring their own computers and chargers. Computers should have at least WIFI preinstalled and a web browser.


This course is over subscribed. However considering the high number of applications received, a next session should be organized by the end of 2019.  You can still apply via this form: https://www.france-bioinformatique.fr/fr/evenements/3586; your name will be added to the waiting list and you will be contacted later.

The registration is free of charge (co-sponsored by the French Bioinformatics Institute and ProFI). This includes course content material and coffee breaks.

Location & Time

Institut des Systèmes Complexes (ISC-PIF), 113 rue Nationale 75013 Paris, FR. Seminar room, 1rst floor. The course will start at 9:00 and end around 18:00. Precise information will be provided to the participants on due time.

Contact: Yves Vandenbrouck