Training for professional insertion and scientific openness

The teaching aims to provide theoretical and practical scientific knowledge in the disciplines related to doctoral research, but also to allow an opening towards other approaches or fields. This need for flexibility is emphasized by the public and private scientific community as an essential element for professional integration. A young recruit is always led to use his or her skills in fields of application that are broader than those of the doctorate.

The curriculum includes 4 mandatory modules of 20 hours each. It is of course possible to combine shorter courses.
  • 2 modules of scientific openness (40h) including the compulsory module of research ethics or scientific integrity
  • 2 modules of professional insertion (40h).

Partial exemption :
Doctoral students under CIFRE contract, active hospital practitioners (e.g.: heads of clinics, AHU), salaried doctoral students whose funding is not dedicated to the thesis or doctoral students in cotutelle, are exempted from half of the modules (40h of training required instead of 80h).


Training modules offered to doctoral students

Mandatory module: training in research ethics and/or scientific integrity
The University of Lyon offers 3 types of doctoral training in research ethics and scientific integrity:

MOOC Research Ethics - FUN platform

Methods: Candidates register directly on the FUN platform. They receive a certificate of attendance from FUN at the end of the course, if they have answered the quizzes.
=> Website:

SPOC Research Ethics (Small private online course)

Exclusively for PhD students of the University of Lyon, it is offered at the same time as the MOOC, on FUN-MOOC.
It will be composed of the same modules and sequences as the MOOC but, in addition, PhD students will have to produce a case analysis (from a case bank) and evaluate 2 case analyses made by their peers.
Modalities: the candidates register on Siged (catalog of transversal trainings), then receive an invitation to connect on the FUN platform.
At the end of the training, a certificate of 18 hours will be issued by the UdL if the final evaluation has been completed.

Research Ethics Training, classic lecture

It is open to doctoral students who have followed the MOOC or SPOC and who wish to go further. Registration on SIGED, training catalog.

MOOC Scientific integrity

Modalities: candidates register directly on the FUN platform. They receive a certificate of attendance from FUN at the end of the course, if they have answered the quizzes.
=> Website :

Internal courses offered by the school

Genomic Sequence Analysis and Phylogeny
The maximum number of students admitted to this module is 16.

* Location: PRABI training room - UMR CNRS 5558; Laboratoire Biométrie et Biologie Évolutive, Bâtiment Grégor Mendel - second   floor; 43, boulevard du 11 novembre 1918; 69622 Villeurbanne Cédex.
* Dates:
* Lecturers: Guy Perrière & Monique Aouad
 * Registration contact: Guy Perrière
>> Link for registration to the training
 * Program :
     o Lecture: Sequence alignment, Molecular phylogeny, Genomics.
     o Practical work: Sequence similarity search, Phylogeny.

Theoretical and practical training in Bayesian statistics

Bayesian inference is increasingly used in various fields of biology (epidemiology, ecology, evolution, etc). The goal of this course is to provide the basics of Bayesian statistics, through a series of 8 sessions of 3 hours, alternating between lectures and practical work on computer.
  • Prerequisites: a basic background in mathematics, as well as a good command of the R programming language.
  • The maximum number of participants admitted to this module is 16 PhD students.
  • Location: PRABI training room - UMR CNRS 5558; Laboratoire Biométrie et Biologie Évolutive, Bâtiment Grégor Mendel - 2ème étage; 43, boulevard du 11 novembre 1918; 69622 Villeurbanne Cédex.
  • Lecturers: Bastien Boussau, Marie-Laure Delignette-Muller, Nicolas Lartillot, Fabien Subtil, Philippe
  • dates, detailed program and registration details: Contact

Paléontologie et Evolution: le message des fossiles

  • Location: UMR 5276 LGLTPE, Université Lyon 1, 69622 Villeurbanne
  • Dates : juin 2019 (dates à préciser), durée 20hContacter le responsable.
  • Lecturers: Fabrice Cordey, Gilles Escarguel, Régis Chirat, Emmanuel Robert, Vincent Perrier
  • Contact : Fabrice Cordey:
In the age of "evolomics" (geno-, transcripto-, proteo-, metabolo-, etc.), what is the point of continuing to study fossils? What do these pieces of rock, witnesses of past evolutions, have to teach us that none of the super-powerful bioinformatics tools now available can see? We first address questions related to the origin of life and the first great eukaryotic radiations, and in particular how the molecular phylogeny of biologists fits - or not - with the available and imperfect data of the fossil record. Four lines of research are then considered and together they draw the same general, phylogenetic and macroecological perspective: the fossils illustrate the "extent of realizations" during the History of Life, specifying in fact the conditions at the limits of the present biosphere, a tiny fraction for more than 3.5 billion years. The last part of the course deals with the biomechanical aspects of biological morphogenesis. Through several examples drawn from the study of animal and plant morphogenesis, we show that the emergence of certain biological forms can be partly predicted on the basis of the study of mechanical instabilities generating similar forms in physical systems.
Finally, the module includes a visit to the paleontology collections of the University of Lyon 1, the first French university collections, created by the Faculty of Sciences of Lyon in 1808, with 10 million specimens! See you in June!

Les outils isotopiques et le cycle de l'eau

Content of the course (18h):
  • Water on earth: 
    • theories about its origin on Earth
    • water: a molecule with extraordinary physical properties
    • water and the origin of life on Earth
    • the water cycle and climate
    • the great reservoirs of water on Earth and their chemical composition
    • water: a resource to be managed by and for human beings
  • Stable isotopes in Earth and Life Sciences:
    • isotopic fractionation mechanisms of light elements (H, C, N, O, S)
    • isotopic tracing of the water cycle and past climates
    • the isotopic memory of fossils:- reconstitution of terrestrial and aquatic living environments- thermophysiology of extinct vertebrates
      reconstitution of diets
    • Tracking migrations: application in paleoanthropology
  • Analytical techniques: 
    • isotopic mass spectrometry
This course will accommodate a maximum of 20 students.

Training in Statistics

Several courses offered at the doctoral school, registration required before October 30. Some modules require pre-requisites such as the participation to another module
(contact : Marie-laure Delignette-Muller, email :

Course content and registration:

Teaching website in biostatistics of VetAgro Sup :

Outils génétiques et construction de mutants chez les micro-organismes

  • Contact : Erwan GUEGUEN, MCU, UCBL,
  • Location: Laboratoire MAP, Bâtiment Lwoff, campus de la Doua, Villeurbanne
  • Dates : May 2-4, 2022
Course Objectives:
Understand and know how to implement the most recent genetic engineering techniques used in bacteria, yeast and microscopic fungi

See the training brochure

Non-specialized M2 master modules

These modules are open to all. Unless you have already taken them, you are free to choose. Interested doctoral students should contact the person in charge of the module concerned in order to find out how to follow the course, and possibly the person in charge of the Master.

Master Health and populations "Linear and non linear mixed effects models"

Resp. René Ecochard

Master Ecology, Microbial Ecology, Evolution (EEME) "Behavioral Ecology"


Master Ecology, Microbial Ecology, Evolution (EEME) "Molecular Phylogeny"


Other courses

The courses offered by the University of Lyon

Consult the programs

Wide range of disciplines represented, from humanities and social sciences to medicine, engineering, technology => registration via SIGED
If you have any questions about these courses (follow-up, registration, certification, etc.), please consult the Siged FAQ or contact

Training courses offered by the URFIST (Unité Régionale de Formation à l'Information scientifique et technique)

Consult the URFIST training catalog 


Internships allowing to learn a technique, to discover another approach to research, as well as internships in companies, can be validated as modules.

Financial support for internships is offered by E2M2

The E2M2 Graduate School offers financial aid for internships abroad and in France. The objective is to help doctoral students to complete a budget in which the research unit or the thesis director would also participate.

This call for proposals does not concern conferences as such but training courses, workshops or seminars intended to provide practical knowledge or to familiarize students with tools used during the thesis.
(NB: these workshops can sometimes take place during congresses).

The maximum amount allocated by E2M2 is 300 euros per project.
These internships can be counted as doctoral training. Priority is given to internships abroad, but applications can also be made for internships in France.

The application form for internship support must be filled out in Word by the doctoral student, signed by the thesis director, and saved as a one-page PDF file with the following name: Forename.Surename.AidesStagesE2M2.pdf

The form should be sent by email to: +