Title Date de début Date de fin Pays Ville Description Site web
Formation CNRS en phylogénie moléculaire 19-03-2019 22-03-2019 France Lyon

Une formation CNRS dédiée à la phylogénie moléculaire se tiendra au Laboratoire de Biométrie et de Biologie Evolutive du mardi 19 au vendredi 22 mars.

Cette formation comprend 50% de cours et 50% de travaux pratiques et les notions qui seront abordées comprennent :

  • Alignements de séquences et recherche de similarités.
  • Modèles d'évolution.
  • Reconstructions phylogénétiques au moyen des méthodes suivantes :
    • Maximum de parcimonie.
    • Distances (minimum d'évolution, neighbor-joining).
    • Maximum de vraisemblance.
    • Inférence bayésienne.
  • Tests (bootstrap, tests de vraisemblance, comparaison de topologies).
Ecole Thématique de Biologie des Systèmes Computationnelle (CompSysBio 2019) 31-03-2019 06-04-2019 France Aussois


We are excited to announce the 3rd Advanced Lecture Course on Computational Systems Biology, that will be held in the Aussois ski resort (France) between March 31-April 6, 2019 (https://project.inria.fr/compsysbio2019/).

The main Course emphasis is methodological. One goal is to illustrate the wealth and diversity of Systems Biology issues for scientists from Computer Science, Mathematics and Physics. Another goal is to allow biologists motivated by Systems Biology to go deeper into methodological issues in order to facilitate their contacts with scientists from the formal sciences.

Sessions are preferentially organized around methodological issues: control theory, dynamical systems, spatio-temporal models, network inference and analysis, evolutionary systems dynamics, with a constant eye on biological relevance (https://project.inria.fr/compsysbio2019/program/). This will be complemented by blackboard teaching and hands-on sessions in parallel classes bearing on specific topics or methods.

The Course will be an opportunity for participants to interact directly with 21 prominent scientists in this rapidly growing field. In order to facilitate casual interactions, there will be time for skiing in the afternoon.

Participants are strongly encouraged to submit an abstract of their current work to be presented as a poster in order to facilitate scientific interactions. Some abstracts will be selected for short talks by the Scientific Committee.

Fellowships are available for pre-PhD students and will be awarded to cover registration fees on the basis of the submitted abstract.

Key dates
Fellowship application: deadline January 25th, 2019
Registration until February 28th, 2019

Elixir Galaxy Community - Workshop at Roscoff 23-04-2019 26-04-2019 France Roscoff


During the first 1.5 days, the attendees will learn about the integration of high-quality tools within Galaxy with their dependencies (Bioconda, Planemo) using the IUC best practice guidelines. They will also learn how to use Galaxy as a training tool and develop training material for the Galaxy Training Network.

The second half of the workshop will be dedicated to Hackathon sessions where attendees will be able to bring their own projects around tool integration and/or training material and develop them collaboratively, with the support of community experts.

Developers, Computing scientists and Bioinformaticians

The workshop participation is free of charge. The ELIXIR Galaxy Community and the IFB/ELIXIR-FR will cover the meeting costs (lunch and dinner)
Travel expenses and lodging need to be covered by each participant individually.

Scientific coordinators and trainers

  • Gildas Le Corguillé (ELIXIR-FR, IFB): Sorbonne Université/CNRS, ABiMS, Station Biologique de Roscoff, France
  • Bérénice Batut (ELIXIR-DE, de.NBI): Freiburg Galaxy team, Backofen lab, University of Freiburg, Germany
  • Anthony Bretaudeau (ELIXIR-FR, IFB): INRA, BIPAA/GenOuest, Rennes, France
  • Björn Grüning (ELIXIR-DE, de.NBI): Freiburg Galaxy team, Backofen lab, University of Freiburg, Germany
  • Loraine Guéguen (ELIXIR-FR, IFB): CNRS/Sorbonne Université, ABiMS, Station Biologique de Roscoff, France
SIB Course: NGS - Genome variant analysis 29-04-2019 30-04-2019 Suisse Bern

We are pleased to announce the SIB course: 

"NGS - Genome variant analysis", on 29 - 30 April 2019, in Bern.

The detection of genetic changes using diverse next generation sequencing technologies  e.g. whole genome, whole exome, RNA and target sequencing has several applications in genomics and other omics fields. The unbiased reliable detection of variants remains a challenge for many.

This two-days course targets biologists and computational biologists. We will mainly introduce and practice the methodology for detecting germline mutations by validating mapping data, realigning regions of interest to reduce false discovery and calling for known variants as well as de novo discoveries.

Further detailed information, prerequisites and application form are available from here.

Should you have any questions, please don't hesitate to contact us at training@sib.swiss.

two SIB courses - Introduction to R Shiny 02-05-2019 06-05-2019 Suisse Lausanne/Zurich

we are pleased to announce two new SIB courses which are going to give an Introduction to R Shiny. They will take place:

- on 2 May in Lausanne

- on 6 May in Zurich

Both courses introduce the R Shiny framework, and provide R programmers with the basic tools to build and deploy their own web apps. Both are one-day courses, their contents are very similar (not to say identical), and are very close in time; all to ease your choice.

They are addressed to biologists, bioinformaticians, and any R users who are interested in developing an interactive web application to communicate their data or analysis to other non-programmers.

Further detailed information, prerequisites and application form are available in the respective links above.

Should you have any questions, please don't hesitate to contact us at training@sib.swiss.


ChIP-seq, RNA-seq et Hi-C : traitement, analyse et visualisation de données 20-05-2019 24-05-2019 France montpellier

- Savoir planifier une expérience simple de type ChIP-seq ou RNA-seq
- Savoir évaluer la qualité des données obtenues dans le cadre de la régulation des gènes (ChIP-seq) et de l'analyse du transcriptome (RNA-seq)
- Maîtriser les principales méthodes et outils d'analyse des données ChIP-seq et RNA-seq
- Savoir les visualiser dans un navigateur de génome et en extraire les coordonnées des pics enrichis
- Savoir manipuler et annoter les fichiers d'enrichissement (bedtools)
- Maîtriser les principales méthodes d'analyse des données Hi-C et de génération des cartes de contact chromosomique
Ingénieurs et chercheurs biologistes / bioinformaticiens

Prérequis : avoir des bases d'utilisation de lignes de commande sous R
1er jour : pre-processing des données ChIP-seq et RNA-seq
- Notions de bases du ChIP-seq, RNA-seq et Hi-C et de leurs pipelines d'analyse, principe de normalisation avec spike-in
- Prétraitement des données (qualité des données brutes, alignements, artefacts de séquençage)
- Exploration des données alignées (estimation de la taille des fragments, qualité de l'alignement)
2ème et 3ème jours : analyse ChIP-seq
- Génération des fichiers d'enrichissement (.wig) avec le package R-PASHA
- Visualisation des fichiers .wig et initiation à la sélection de régions enrichies, aux paramètres de détection (MACS2 ou directement sur genome browser)
- Initiation à la mise en place de métaprofils autour des régions d'intérêt (gène, TSS, TES, enhancers)
- Analyse d'enrichissement d'annotations fonctionnelles ("gene ontology")
- Recherche de motifs dans les régions enrichies
Analyse RNA-seq
- Quantification de l'expression des gènes dans les données RNA-seq à travers le RPKM
- Principe de normalisation utilisant des spike-in
- Analyse de l'expression différentielle des gènes et des exons
4ème jour : analyse Hi-C
- Traitement et alignement des séquences et construction de la carte de contact chromosomique
- Visualisation et interprétation de la carte de contact
- Présentation de quelques bases de données et d'outils de visualisation de Hi-C
- Discussion (3 h) sur les problématiques des participants et sur les pistes de solutions à y apporter
Alternance de cours (4 h) et de TD (24 h)
Mise à disposition d'un ordinateur par stagiaire sous linux avec logiciels nécessaires à la formation

EMBO Bioinformatics and genome analyses course 2019 16-06-2019 30-06-2019 Italie San Michele all'Adige

This EMBO Practical Course will cover a range of genome analyses and their fundamental elements.

The first principal theme of the course is comparative genomics, covering genome analysis and exploration, pair-wise and multiple comparisons of genomes and evolutionary inferences (orthologs, paralogs and their classification).

The second principal theme of the course is related to Next-Generation Sequencing data analyses, including sequence assembly methods, metagenomics and its applications as well as genomic structural variants.

Application is through the EMBO web site:

Deadline for application is March 31, 2019.

Course Poster can be downloaded from this link:

MODÉLISATION FORMELLE DE RÉSEAUX DE RÉGULATION BIOLOGIQUE (École CNRS) 23-06-2019 28-06-2019 France Ile de Porquerolles


Les méthodes formelles issues de l'informatique se sont avérées très efficaces pour modéliser les réseaux de régulation biologique et élucider les liens de causalités entre interactions moléculaires d'une part, et phénotypes biologiques d'autre part.

La modélisation formelle des réseaux de régulation biologique participe activement aux avancées en « biologie des systèmes » et en « biologie synthétique » qui sont devenues des thèmes prioritaires de recherche pluridisciplinaire entre biologie, informatique, mathématique et physique-chimie théorique.

Il s'avère que la communauté francophone est à la pointe de la recherche mondiale dans ce domaine et cette école, francophone, présente une palette complète des différents cadres de modélisations (un par demi-journée). Les modalités pédagogiques ouvrent de nombreuses plages durant lesquels les participants interagissent largement avec les intervenants.

International Summer School on Networks and Evolution, 3rd edition 23-06-2019 29-06-2019 France Roscoff

Introduction to the concepts and methods of networks in evolutionary studies (sequence similarity networks, genome networks and multipartite graphs)

This free summer school will be held in Roscoff, France, between June 23rd 2019 (date of arrival) and June 29th (date of departure).

This school is designed in priority for biologists and bio-informaticians (completing a PhD degree or currently post-doctoral fellows, as well as researchers), who wish to learn the bases of network analyses.

The main notions (regarding various types of networks, the relevance of their analyses, and some bases in graph theory) will be introduced by short theoretical classes, followed by practical case-studies, introducing the basics in programming required to run such network analyses as well as to use the existing software/tools. Our goal is that, by the end of this summer school, all applicants will be qualified to perform network analyses of their own datasets.

More precisely, we will focus on the following concepts and methods:

- Introgressive evolution and large-scale diversity studies.

- Construction and analysis of sequence similarity networks (construction and sorting of connected components, definition of gene families, search for composite genes, implementation of centrality measures)

- Construction and analysis of genome networks (construction of weighted genome networks, implementation of their diameter, shortest paths, analyses of labeled nodes, etc.)

- Construction and analysis of gene-genome bipartite graphs (detection of connected components, and their articulation points, and twins)

In addition, 9 conferences on networks and evolution will be delivered by leading European and North American scientists during this school.

Confirmed speakers (complete list):

Pr. JP Gogarten (UConn, USA): Lateral Gene Transfer and Prokaryotic evolution

Pr. Robert Beiko (Dalhousie University, Canada) : Introduction to phylogenetic networks

Dr. Eric Bapteste (UPMC, France): Introduction to sequence similarity networks

Pr. Debashish Bhattacharya (U. Rutgers, USA): Reticulate evolution in eukaryotes

Pr. Eugene Koonin (NCBI, USA) : Viruses and networks

Pr. Michel Habib (LIAFA, France): Networks and centralities

Dr. Damien Eveillard (U. Nantes, France): Co-occurrence networks and the evolution of geochemical cycles in the environment

Pr. Daniel Huson (U Tuebingen, Germany): Network approaches in microbiome analysis

Pr. Marc-André Sélosse (MNHN, France): The living world as a network

This summer school is funded by ERC grant (FP7/2007-2013 Grant Agreement # 615274). Hence, registration is free, housing and food (breakfast, lunch) are also fully covered. Applicants will only need to fund their travel to Roscoff and their evening dinners.

10 places only are available, with a mandatory requirement: applicants must show basic computer skills (i.e. to be familiar with Linux environment and with at least one programming language, preferably Python).
Applications are to be submitted asap, and no later than February 15th 2019, by email to :

eric.bapteste@upmc.fr , and contain a brief letter describing why this class will be of significant interest for the applicant and his/her future studies.

Applicants will be selected based on their motivation, and their resume, including the names of two scientific referees for PhD and postdoctoral fellows.

We are excited to meet you soon in Roscoff.

Eric Bapteste + Philippe Lopez + Eduardo Corel

eX Modelo summer school on simulation model exploration 23-06-2019 28-06-2019 France Châtenay-sur-Seine

eX Modelo is a research school on the exploration of simulation models (sensitivity analysis, calibration, validation, etc.) that will be held from June 23 to 28, 2019 in a rural setting 1 hour from Paris.

This thematic school is intended for postgraduate students, engineers, academic researchers and companies interested in modelling, whatever their scientific field. The objective is to teach participants to become autonomous in exploring their models, in a friendly environment.

The courses, labs and feedback will be lead by a network of researchers who have a recognized expertise in these transdisciplinary practices.

During this week of training, you will discover step by step advanced methods for model exploration. There will be theoretical sessions as well as practical group workshops on adapted case studies.

The OpenMOLE platform (https://www.openmole.org), specially dedicated to the exploration of numerical models, will be used throughout the week to facilitate the understanding and implementation of practical cases.

SysBioCancer2019: 2nd course on Computational Systems Biology of Cancer: Single Cell Analysis 23-09-2019 28-09-2019 France Paris

We are glad to announce the second international multidisciplinary course entitled ‘Computational Systems Biology of Cancer: Single Cell Analysis’.

SysBioCancer2019 - Institut Curie, Paris, France



Course objective

To improve interpretation and use of omics data that nowadays are accumulated in any biological or medical lab.  This year, the course will particularly focus on SysBio approaches for single cell data analysis. We will review current methods and tools for the analysis and interpretation of single cell data, along with concrete applications related to cancer. In particular, we will emphasize the role of single cell data research for understanding the heterogeneity of tumor.