Former trainings – C3BI

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Former trainings


Starting Mon 3 Dec 2018 – Hands-on microbiome data analysis: tools for understanding microbial communities in health and disease
Gregorio Iraola

This course aims to provide the theoretical and practical concepts for standard bioinformatic analysis in the field of microbiome research. The course will focus on the application of state-of-the-art software tools for the analysis of environmental and host-associated microbiomes, with particular emphasis on understanding how they change or constitute a risk for human health. The course will have expert lectures and theoretical/practical data analysis sessions with real datasets. STUDENT’S PRE-REQUISITES • Directed to post-graduation (M.Sc. or Ph.D.) students. • Basic concepts of high-throughput sequencing technologies. • Basic understanding of metagenomics and microbial ecology. • Basic skills in the Linux terminal. DEADLINE APPLICATIONS October 19, 2018. Send your CV (one page) and letter of motivation to: antonio.borderia@pasteur.fr

Starting Mon 22 Oct 2018 – C3BI Courses: Introduction to Molecular Phylogenetics – Hong Kong 2018
Olivier Gascuel

General Information: This introductory course aims to give the basic theoretical and practical concepts, best practices, and software necessary to start working on molecular phylogenetics and its applications to epidemiology. The course will have theoretical morning sessions followed by small groups practice for a few selected students with their own data. Flyer for the course: CLICK ME Topics: Introduction to phylogeny: General principles for the inference, interpretation of trees, and application to infectious diseases Introduction to the math behind the trees and evolutionary models Distance and parsimony methods Maximum likelihood methods Bayesian methods, phylodynamics Branch supports, bootstrapping How to select the best method and evolutionary model Tree dating, reconstructing and using character evolution Molecular epidemiology Teachers: Chair: Olivier Gascuel, C3BI, Institut Pasteur (France) Anna Zhukova, C3BI, Institut Pasteur (France) Frédéric Lemoine, C3BI, Institut Pasteur (France) Hein Min Tun, School of Public Health, The University of Hong Kong Julien Guglielmini, C3BI, Institut Pasteur (France) Sebastian Duchene, University of Melbourne (Australia) Tim Vaughan, ETH Zürich (Switzerland) Tommy Lam, School of Public Health, The University of Hong Kong Veronika Boskova, ETH Zürich (Switzerland) Course dates: Monday, October 22nd to Saturday, October 27th Pre-requisites: Basic knowledge on how to use sequence databanks Basic knowledge using Blast and multiple alignments software Basic knowledge on statistics (tests, distributions, parameter estimation) Applications: Open to postgraduate students, MD, DVM, postdoctoral fellows and young scientists from Hong Kong and overseas. The course fees are 500HK for the theory sessions and 1000HK for the full course. Students coming from the Institut Pasteur international Network will have the fees waived. Please fill in the following application form before August 7st Midnight (HK time). Use the link if you can’t see the embedded form: https://goo.gl/forms/rgYrUNrEz6rqgELP2)

Starting Mon 25 Jun 2018 – Linking gene and function, comparative genomics tools for biologists
Valerie Crecy-Lagard

More than twenty years after the first bacterial genome has been sequenced, microbiologists are faced with an avalanche of genomic data. However, the quality of the functional annotations of the sequenced proteome is very poor with more than half of the sequenced proteins remaining of unknown function.

With nearly 80,000 whole genomes sequences available and increasing amount of post-genomics experimental data available, it is possible to gather different types of information that lead to better functional annotations and can guide the experimental process. The workshop will guide the attendees through practical examples and show them an array of tools and databases that they can apply directly to their research problem.

No prior programming experience is required, all the tools available can be used through graphic user interfaces.

For background read (https://www.ncbi.nlm.nih.gov/pubmed/20001958)

Starting Mon 19 Mar 2018 – Analyse de séquences
Corinne Maufrais

OBJECTIFS : Les biologistes sont régulièrement confrontés à des gènes (ou des protéines) de fonctions inconnues ou mal annotés. Dans ce contexte, maîtriser quelques techniques basiques d’analyse de séquences peut se révéler d’une aide précieuse. L’objectif de cette formation est de présenter, au travers de l’utilisation de sites web spécialisés, quelques grands principes sur l’analyse de séquence. L’ensemble de la formation combine exposés théoriques (fondements méthodologiques des programmes) et applications pratiques (mise en relation des notions théoriques avec les paramètres des programmes et les résultats obtenus) pour permettre une utilisation autonome et critique de quelques logiciels d’analyse des séquences biologiques. DATE ET LIEU : Les cours auront lieu du lundi 19 mars au vendredi 23 mars de 9h30 à 12h30 et de 14h à 17h MODULE 4/ Salle 3 sous la cantine. INSCRIPTION : Répondre à cette annonce avant le 9 Mars 2018 en envoyant un email à corinne.maufrais@pasteur.fr AUDIENCE : Ce cours s’adresse à toutes personnes voulant améliorer sa maitrise des outils d’analyse de séquence dans le contexte du laboratoire : technicien, ingénieur, doctorant, postdoc, chercheur. Il n’est pas demandé de prérequis en informatique, la totalité des travaux pratiques se fera à l’aide de sites internet sans utilisation d’Unix ou de lignes de commandes. La formation sera donnée en français.   PROGRAMME : 1er jour : – Matin : Introduction générale et Organisation des banques de données publiques – Après-midi : Recherche d’information dans les banques de données publiques 2ème jour – Matin : Comparaison et alignement de deux séquences (Cours) – Après-midi : Découverte de logiciels d’alignement de séquences : dotplot, water, needle, diffseq, lastweb (TP) 3ème jour – Matin : Recherche de séquences similaires dans les banques de données et utilisation de Blast (Cours + TP) – Après-midi : Comparaison et alignement multiple de séquences avec clustalO, needle, t-coffee … (Cours + TP) 4ème jour – Matin : (Cours + TP) o Recherche et extraction de motifs (pattern/profils/HMM/logo) o Découverte de familles de protéines et domaines fonctionnels dans la banque prosite. – Après-midi : Introduction à l’annotation de génome (Cours + TP) 5ème jour : – Introduction à la phylogénie (Cours + TP)

Starting Mon 27 Nov 2017 – Hands on Bogota
Institut Pasteur and UniAndes

The University of Los Andes and the Hub of Bioinformatics and Biostatistics of the C3BI (Center of Bioinformatics Biostatistics and Integrative Biology) at Institut Pasteur will organize this Hands-on course aimed at students/researchers that have produced HTS data sets and would like to learn how to get the most out of it. This course will provide a general introduction to the bioinformatic and statistical aspects of HTS data analysis, alternating theory and practice. The objective is to present the general concepts such as file formats, mapping of sequences, as well as, the specific procedures for each data type: DNA-Seq, RNA-Seq, ChIP-Seq. An additional session will be devoted to the pathway and functional analysis for gene set issued from differential or other kind of analysis. Knowledge of the basic Linux and R commands is highly recommended. Otherwise it is advisable to follow the introductory tutorial available on the course web page. Please be aware that the workshop will be delivered both in Spanish and English.

Starting Mon 6 Nov 2017 – C3BI Hands-on NGS course Hong-Kong 2017
C3BI Training

This theoretical and practical course is aimed at researchers who would like to get the most out of their Next Generation Sequencing datasets. We will tackle several topics, encompassing theoretical NGS approaches and statistical analysis of NGS data. Ultimately, we want this course to be of immediate value to the students. The first week of this course (Nov 6th – 10th) will be devoted to theory and practical examples for a broad audience, while the second week (Nov 13th – 17th) will be dedicated to practical analysis and hands-on for a selected group of participants. Prospective students when registering can apply for the first theoretical week only or for both weeks. Students applying for the hands-on section will be selected based on their data and the analyses they wish to perform. The course will be free for participants coming from the Institut Pasteur International Network, whereas all other students will pay 1000HKD if they assist to the first week and, 2000HKD if they take the whole course. The course will be held at the University of Hong-Kong. The official language for the theoretical and hands-on session will be English. This hands-on NGS course is open to the whole Pasteur International Network, Hong- Kong Universities and Research Centers.

Starting Tue 24 Oct 2017 – Linking gene and function, comparative genomics tools for biologists.
Valerie Crecy-Lagard

More than twenty years after the first bacterial genome has been sequenced, microbiologists are faced with an avalanche of genomic data. However the quality of the functional annotations of the sequenced proteome is very poor with more than half of the sequenced proteins remaining of unknown function. After taking this course, students should master an array of web-based tools to help to predict gene function. This will allow them to generate in silico based functional predictions and produce illustration for manuscripts that use comparative genomic methods.

Starting Mon 16 Oct 2017 – Introduction to data analysis 2017-18
c3bi team

This five weeks graduate level course will give participants basic skills and hands-on training in biostatistics. It will cover all the steps of an analysis workflow : design, collection, curation, hypothesis testing and data mining. The course can be divided into four different topics whose practice is mandatory for those seeking to implement a relevant analysis workflow. Thus, it will cover basics and practice in unix, text file management, R and biostatistics. We will focus on the topics useful for scientists working in a wet lab: experimental design, hypothesis testing, production of good scientific plots. IDAprocess Course schedule : The course will take place from January 16th to February 17th 2017, with two-hour lectures every day. Two sessions are provided:
  • session 1 from 9 AM to 11 AM
  • session 2 from 11 AM to 1 PM.
Course location : Lectures will take place in Amphi Jacques Monod. Please note On Fridays, lectures will take place in the Bâtiment François Jacob, room 28-01-01A. On February 10th and 17th they will take place in the afternoon, from 1:30 to 3:30 for session 1 and from 3:30 to 5:30 for session 2.

Starting Mon 25 Sep 2017 – Hands-on Metagenomics data analysis: tools for bioprospection in clinical and environmental microbiology
Gregorio Iraola

The main objective of this training course is to provide the trainees: i) a concise theoretical framework of the state-of-the-art methodologies and analytical approaches to analyse metagenomic high-throughput data and ii) help and assist the trainees during intensive hands-on sessions to apply these methodologies on their own real datasets and answer their own scientific questions. Furthermore, the course will be an opportunity for the trainees to meet international experts in the area, generating a highly motivating and synergistic environment for incorporating new knowledge, setting up collaborations, answering questions and asking new ones.

Starting Mon 3 Apr 2017 – Bioinformatics of protein­protein interactions for wet lab scientists
C3BI Teams

Understanding physical and functional interactions between molecules in living systems is crucial in many biological processes. Several powerful methods and techniques have been developed to generate molecular interaction data, focusing mainly on protein­protein interactions (PPIs). In particular, PPIs involving partially or completely unstructured regions are building blocks of regulatory and signalling networks that control cell response to external and internal cues. Exploring these interactions may help understanding a protein’s function and behavior, predicting biological processes that a protein of unknown function is involved in, and characterising protein complexes that can be used to modulate or perturb known biological processes and pathways.

Starting Mon 20 Mar 2017 – Scientific programming in Python
Training Team



Starting Mon 16 Jan 2017 – Introduction to data analysis
Teaching Team

soon …

Starting Mon 21 Nov 2016 – Hands-on NGS course Paris
C3BI Teams



Starting Mon 14 Nov 2016 – Introduction à la Phylogénie Moléculaire : CONCEPTS, METHODES ET OUTILS
Catherine Dauga

Le C3BI propose des cours pour acquérir les notions théoriques de phylogénie et maitriser les outils et logiciels. Les cours d’”Introduction à la phylogénie moléculaire” sont ouverts à tous (inscription obligatoire pour les cours et travaux pratiques dans la limite des places disponible). Il est possible de ne s’inscrire que pour la partie théorique. Ces cours sont dispensés en langue française. Lundi 14 Novembre (9h30-12h30): Présentation des principales banques de données et BLAST Mardi 15 Novembre: (9h30-11h00): Alignements Multiples Mercredi 16 Novembre (9h30-11h00): Introduction à la Phylogénie Jeudi 17 Novembre (9h30-11h00): Modèles d’évolution Vendredi 18 Novembre (9h30-11h00): Approches par Maximum de Parcimonie Lundi 21 Novembre (9h30-11h00): Méthodes de Distance Mardi 22 Novembre (9h30-11h00): Méthodes de Vraisemblance Mercredi 23 Novembre (13h30-15h00): Reconstruction Phylogénétique & Approches Bayésiennes Jeudi 24 Novembre (9h30-11h00): Inférence des Forces Sélectives Vendredi 25 Novembre (9h30-11h00): Choix des Méthodes et Interprétation programme complet inscription par mail à formation@pasteur.fr + formulaire https://docs.google.com/forms/d/1BLfI211EwW7h4CxVRetaK84LuwCGCly_wAxJzfw3UL0/viewform?edit_requested=true

Starting Tue 18 Oct 2016 – Web-based tools to analyse and interpret high-throughput biological data
Hedi Peterson

Overview. In this course we introduce web-based tools to analyse and interpret high-throughput biological data. In the main focus will be g:Profiler – a toolset for finding most significant functional groups for a given gene or protein list; MEM – a query engine allowing to mine hundreds of public gene expression datasets to find most co-expressed genes based on a query gene; and ClustVis – a web tool for visualizing clustering of multivariate data using Principal Component Analysis plot and heatmap. Audience. Biologists and bioinformaticians who are dealing with high-throughput gene expression data or other high-throughput data and would like to learn state-of-the-art methods for mining and analysing such data. Learning objectives. g:Profiler – learn how to perform gene set enrichments analysis and find what are the most significant functional groups in your gene or protein list (for example interesting genes/proteins from Q-RT-PCR or RNA-seq experiment results). To learn how to convert gene and protein IDs from one namespace into another or find corresponding gene/protein IDs from another organism. MEM – learn to perform and interpret MEM co-expression queries. Given a query gene, MEM performs co-expression analysis across hundreds of public datasets and returns ordered list of globally similar genes. We’ll learn how MEM can be used to infer potential function for a gene based on other genes that are globally similar. For a gene pair we’ll learn how to identify the datasets and conditions where they behave similarly and where they do not. ClustVis – learn how to make exploratory data analysis plots using ClustVis web tool. How to prepare a dataset for uploading the data or search among publicly available datasets. We learn how to filter a chosen dataset using ClustVis and how to choose pre-processing options. We will learn how PCA plot and heatmap can be modified and how to interpret and export the results. Prerequisites. Common understanding of high-throughput technologies does help to follow the lectures. Access to web browser is required.

Starting Mon 3 Oct 2016 – INDA Hands-on NGS-Statistics course, Senegal 2016
INDA Team

This theoretical and practical course is aimed at researchers that would like to get the most out of their Next Generation Sequencing datasets. We will tackle several topics, encompassing theoretical NGS approaches and statistical analysis of NGS data. The first week of this course (Oct 3rd – 7th) will be devoted to theory and practical examples for a broad audience (100 participants), while the second week (Oct 10th – 14th) will be dedicated to practical analysis for a selected group (30) of participants. Prospective students for the hands-on section should apply and will be selected on the basis of their data and the analyses they wish to perform. The exact syllabus will depend on the interest of the attendees; we want this course to be of immediate value. The course will be held in Mbour in the AIMS Senegal facilities. The official language for the theoretical and hands-on session will be English. This hands-on NGS course is open to the whole Institut Pasteur International Network, Senegalese Universities (CEA-MITIC), H3ABioNet and AIMS Senegal.

Starting Mon 12 Sep 2016 – Summer School 2016 in Metagenomics
French Institute of Bioinformatics, France Génomique and Institut Pasteur .

Metagenomics, the sequencing of DNA directly from a sample without first culturing and isolating the organisms, has become the principal tool of “meta-omic” analysis. It can be used to explore the diversity, function, and ecology of microbial communities. The aim of these 4 days workshop will be to give researchers and students an overview of the tools and bioinformatics techniques available for the analysis of next generation sequence data from microbial communities. Its content will focus on the taxonomic assignment and the functional analysis of metatranscriptomic and metagenomic data. The format will comprise a mixture of lectures and hands-on practical tutorials where students will process example data sets in real-time.

Starting Tue 10 May 2016 – Introduction to NGS data analysis
HUB team

The Hub of Bioinformatics, Biostatistics and Integrative Biology at the Institut Pasteur organizes thematic courses open to everybody. The second session, entitled “Introduction to NGS data analysis” will take place every Tuesday, from the May 17th to June 28th 2016, in the room Retrovirus No. 14, at the ground floor of Lwoff building. This course will provide a general introduction to the concepts of sequencing data analysis, alternating theory and practice on various data types: DNA-Seq, RNA-Seq, Chip-Seq, Metagenomics and HiC. The course is aimed at people who want to get familiarized with the concepts and tools used for the analysis of sequencing data. The objective is to present the basic concepts such as file formats, mapping of sequences as well as the specific procedures for each data type. Participants are asked to come with a fully charged laptop (not enough plugs available) with the required tools already installed (ssh connection client). The list of required software will be available on the course web page ten days before the start of the session. This course is an introduction to sequencing data analysis. Knowledge of the basic Linux command lines is highly recommended. Otherwise it is advisable to follow the introductory tutorial available here (https://cours.web.pasteur.fr/unix/unix-I/#1) and on the course web page.

Starting Tue 8 Mar 2016 – Morning sessions – Experimental data analysis using R
Marie-Agnès DILLIES

Le Hub de Bioinformatique et Biostatistiques de l’Institut Pasteur organise des cours thématiques ouverts à tous. La première session intitulée « Analyse exploratoire des données avec R » aura lieu du 7 mars au 18 avril, tous les lundi matin de 9h à 12h en salle rétrovirus, Bâtiment Lwoff. Les cours sont donnés en français. L’inscription est gratuite mais obligatoire pour les non pasteuriens.

Starting Mon 30 Nov 2015 – Leishield – Training Course on Next Generation Sequencing
HUB team

The primary aim of this course was to provide a basic understanding of the Leishmania genome, NGS technology and analysis tools, and to develop a basic pipeline for the students to start working on their data. This first pipeline will help to standardize all analysis done in the consortium and should facilitate a posterior paper publication. This pipeline will evolve in the context of a collaboration between the Leishield partners and the C3BI, taking into account the difficulties to analyze and interpret the sequence data generated, and the specific needs of each Consortium node. A future Workshop will be organized in June 2016 to tackle all these questions, and to have a follow-up on the analysis. The secondary aim of this course was to have a first contact between the C3BI and Leishield in order to establish a future collaboration. This course provided to the teachers and students, fertile ground to work together and exchange ideas.

Starting Thu 8 Oct 2015 – Current sequencing methods , bioinformatics problems related to high throughput methods


Understand some principles behind NGS Understand the uses of NGS data in: Whole genome assembly; Gene expression analysis; Genome annotation; Gene regulation analysis; Variation studies Understand NGS data formats and file handling Understand Quality control of NGS data Understand Assembly and mapping of NGS data

Starting Thu 8 Oct 2015 – Méthodes actuelles de séquençage, problèmes bioinformatiques liés aux méthodes à haut débit


Connaitre les différents apports et limites des méthodes de séquençage actuelles . Mieux appréhender les problématiques de bioinformatique lié à l’utilisation du “big data”

Starting Tue 29 Sep 2015 – Introduction à la phylogénie moléculaire


Le C3BI propose des cours pour acquérir les notions théoriques de phylogénie et maitriser les outils et logiciels. Les cours d'”Introduction à la phylogénie moléculaire” sont ouverts EN ACCES LIBRE à tous les Pasteuriens et dispensés en langue française (pas d’inscription). Ils auront lieu du 29 septembre 2015 au 02 octobre 2015 en salle Rétrovirus du bâtiment Lwoff (sauf le 29/09 après-midi : salle Duclaux 2e étage). ** Mardi 29 septembre – 9h30-11h : Méthodes de distance (A. Criscuolo) – 14h-15h30 : Méthodes de Maximum de Parcimonie (O. Gascuel) ** Mercredi 30 septembre – 9h30-11h : Modèles d’évolution (O. Gascuel) – 14h-15h30 : Méthodes de Maximum de Vraisemblance (O. Gascuel) ** Jeudi 1er octobre – 9h30-11h : Méthodes Bayesiennes (G. Perriere) – 14h-15h30 : Inférences des forces sélectives (G. Perriere)

Starting Mon 28 Sep 2015 – Acquisition de données théoriques et maîtrise d’ourils pour la phylogénie


– Acquisition de notions théoriques concernant la phylogénie – Maîtrise des outils et logiciels pour la phylogénie Consulter la page: http://webcampus.pasteur.fr/jcms/c_380246/formations-sur-le-campus#Phylogenie_Moleculaire2015

Starting Fri 25 Sep 2015 – Banques de données et Alignement Multiple (pour la phylogénie)


Acquisition de notions théoriques et pratiques concernant l’interrogation des banques de données et les alignements multiples en phylogénie

Starting Tue 15 Sep 2015 – Notions Fondamentales en statistiques


Etre capable de décrire une série de valeurs. Poser correctement les problèmes que les statistiques peuvent résoudre. Savoir choisir et mettre en oeuvre le test statistique adapté à chaque situation. Savoir interpréter les sorties logicielles correspondantes.

Starting Thu 10 Sep 2015 – INDA Hands-on NGS-GWAS course


The objective is to provide to each student the knowledge and tools necessary to understand and analyze Next Generation Sequencing (NGS) data, as well as Genome-wide association studies (GWAS), no matter the dataset they have or where they come from in the RIIP. The course is around two weeks long. First week is devoted to theory sessions that will include the basis of NGS technologies, quality analysis, algorithms for mapping and assembling, different kinds of biological experiments and a strong focus on the corresponding statistical techniques. We will also offer and introduction to GWAS, Genotypic variation and linkage disequilibrium, and SNP array design, with some model cases. The second week is dedicated to practice, in which the students work with their own data in small groups with a mentor that guides them. The practice week is designed so the course is of immediate use to each student. We expect the students to go back to their countries with the necessary knowledge to continue working on their own data. Lastly, this course will also promote interactions through bioinformatics between different Institut Pasteur in the RIIP. We will only accept candidates coming from Institut Pasteur International Network , Fiocruz, and the University of Sao Paulo (USP). Candidates must fill and send the application form, a short CV (2 pages max) and a letter of support from your head of laboratory or mentor to the following email: inda_training@pasteur.fr Deadline for the application is July 31st, 2015 at midnight (Paris time).