C3BI Courses: Introduction to Molecular Phylogenetics – Hong Kong 2018

EVENT : C3BI Training


Main speaker: Olivier Gascuel, from C3BI, Institut Pasteur (France) Date : 22-10-2018 at 09:00 am Location: Institut Pasteur International Network – HKU Pasteur – Hong Kong


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 of 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 20th Midnight (HK time). Use the link if you can’t see the embedded form: https://goo.gl/forms/rgYrUNrEz6rqgELP2)

Training – C3BI Hands-on NGS course Hong-Kong 2017

EVENT : C3BI Training

C3BI Hands-on NGS course Hong-Kong 2017


Main speaker : C3BI Training, from Institut Pasteur Date : 06/11/2017 at 09:00 am Location : Other – HKU-Pasteur Research Pole


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.

Please fill the application form HERE, and send your CV and 1-2 letters of recommendation to hku-pasteur@hku.hk

Deadline for applications: September 1st, 2017 (midnight Paris time) For more information, please contact the course secretariat at hku-pasteur@hku.hk
Course Documents

Training – Hands-on Metagenomics data analysis: tools for bioprospection in clinical and environmental microbiology

EVENT : C3BI Training

Hands-on Metagenomics data analysis: tools for bioprospection in clinical and environmental microbiology


Main speaker : Gregorio Iraola, from Institut Pasteur Montevideo Date : 25/09/2017 at 10:00 am Location : Other – Institut Pasteur Montevideo,Institut Pasteur, Paris


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.

Please click on the flyer below for more information:


Training – Web-based tools to analyse and interpret high-throughput biological data

EVENT : C3BI Training

Web-based tools to analyse and interpret high-throughput biological data


Main speakers : Dr. Hedi Peterson and Dr. Priit Adler, from University of Tartu, ELIXIR Estonia Date : 18/10/2016 at 02:00 pm Location : Bime meeting room 28-01-01A – BIME (28) ,Institut Pasteur, Paris


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. Please bring a laptop, to be able to use the tools. Participants are very welcome to bring their own gene/gene list of interest, to analyse them during the session.


Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting

  elixir_paris_ad Enregistrer Enregistrer

Training-INDA Hands-on NGS-Statistics course, Senegal 2016

EVENT : C3BI Training


Speaker : INDA Team, from Institut Pasteur From : October 3rd 2016 To : October 14th 2016 Location : Mbour, Senegal,Institut Pasteur, Paris


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.


More about this training here

 

Ecole thématique – Bioinformatics of protein­-protein interactions for wet lab scientists

ppi-logo_V2

About

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 protein­-protein 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.

The course is intended for PhD students and postdocs working in experimental biology, but scientist of all levels are welcome. Participants will be introduced to a wide variety of popular bioinformatic tools aimed at exploring and predicting PPIs. At the end of the course, participants should have an increased ability to:
  • Find and use information on PPIs from diverse databases.
  • Visualise and inspect 3D structure of PPIs and PPI networks.
  • Predict protein modules such as globular domains, unstructured regions and short linear motifs (LMs), from the protein sequence.
  • Portray the characteristics of PPIs between different types of protein modules.
  • Become acquainted with current strategies to target PPIs for drug design.
The course is structured in lectures and practical sessions (hands-on). Practical sessions are optional but highly advised. They will include the following applications:
  • Biological database searches for information on PPI data associated to any protein of interest: UniProt, MINT, ePDB/PDB, among others.
  • Exploration of PPI networks: STRING, STITCH, Cytoscape.
  • Identification of residues responsible for the physical contact between proteins in PPIs using CLUSTALX, JalView, PyMOL, PISA.
  • Prediction of protein interaction modules from protein sequence: using resources such as ELM, IUPRED, Anchor.
Application deadline

15 January 2017

Selected participants will be notified by

Early February

Apply now!

Speakers

Organizing Committee

Programme

Download the final schedule  
  • 09:00 – 10:00 Registration.
  • 10:00 – 11:15 Overview of experimental techniques to map PPI (Daniel Ladant)
  • 11:15 – 11:45 Coffee break
  • 11:45 – 13:00 PPI dedicated databases (Javier de las Rivas)
  • 13:00 – 14:00 Self organized lunch
  • 14:00 – 15:30 Hands on: Databases and ­tools for PPI visualization and analysis (Javier de las Rivas, Freddy Cliquet)
  • 15:30 – 16:00 Coffee break
  • 16:00 – 17:30 Hands on: Databases and ­tools for PPI visualization and analysis (Javier de las Rivas, Freddy Cliquet)
  • 17:30 – 18:30 Welcome get together – Poster session
  • 09:00 – 10:15 Structural modelling of protein-protein interactions using evolution (Raphaël Guerois)
  • 10:15 – 10:45 Coffee break
  • 10:45 – 12:00 Large-scale cross-docking to unravel protein-protein interactions: explored directions and progress (Alessandra Carbone)
  • 12:00 – 14:00 Self organized lunch
  • 14:00 – 15:30 Information-driven modelling of biomolecular interactions (Alexandre Bonvin)
  • 15:30 – 16:00 Coffee break
  • 16:00 – 17:30 Hands on: Protein-protein docking with HADDOCK (Alexandre Bonvin)
  • 17:30 – 18:00 Flash talks from participants
  • 09:00 – 10:15 Diversity of PPIs, modular protein architecture and the nature of cell regulation (Toby Gibson)
  • 10:15 – 10:45 Coffee break
  • 10:45 – 12:00 Protein disorder prediction and dedicated databases (Zsuzsanna Dosztányi)
  • Free afternoon
  • 09­:00 – 10:30 Hands on: Linear motifs (LMs) resources and methods for LMs prediction (Toby Gibson)
  • 10:30 – 11:00 Coffee break
  • 11:00 – 12:30 Hands on: LMs resources and methods for LMs prediction (Toby Gibson)
  • 12:30 – 14:00 Self organized lunch
  • 14:00 – 15:30 Hands on: IUPRED, ­ ANCHOR, DisProt, D2P2 (Zsuzsanna Dosztányi)
  • 15:30 – 16:00 Coffee break
  • 16:00 – 17:30 Hands on: IUPRED, ­ ANCHOR, DisProt, D2P2 (Zsuzsanna Dosztányi)
  • 17:30 – 18:00 Flash talks from participants
  • 09:00 – 10:15 Considering protein interactions with smaller proteins: Protein-peptide interactions (Pierre Tufféry)
  • 10:15 – 10:45 Coffee break
  • 10:45 – 12:00 In silico drug design on protein-protein interactions (Olivier Sperandio)
  • 12:00 – 14:00 Self organized lunch
  • 14:00­ – 15:30 A journey into structural disorder and induced folding in paramyxoviruses: an experimental perspective (Sonia Longhi)
  • 15:30 – 16:00 Coffee break
  • 16:00 – 17:00 Concluding remarks / Round table
  • 17:00 – Social event

Course Material

Click the following link to access Course Material (restricted access)

Registration

Registration is compulsory yet free of charge. During the registration process you’ll need to specify whether you want to take the full course, i.e. assist to both theoretical and practical sessions, or just participate in the theoretical sessions. Selected participants of the full course are encouraged to present a poster or a 5 minutes talk (flash talk) on their research subject.

Registrations are close now

Contact

contact-c3bi@pasteur.fr
+ 33 1 45 68 80 00

Location

INSTITUT PASTEUR
25-28, rue du Docteur-Roux
75724 Paris Cedex 15, France
Metro Pasteur

Lectures : Retrovirus room – Lwoff Building
Hands-on : Room 3 – Social Building

Map of the campus  

Practical information

Enregistrer

Training – Morning sessions – Data analysis using R – Starting 8th March 2016

EVENT : C3BI Training – Morning sessions


Trainers : Marie-Agnès Dillies, Anne Biton, Stevenn Volant, Hugo Varet, from Bioinformatics and Biostatistic Hub, Felix Cheysson from Unité de pharmacoépidémiologie et maladies infectieuses, Institut Pasteur, Paris Time : 09:00 am – 12:00 am From : 08/03/2016     To: 12/04/2016 Every Tuesday

Location : Retrovirus room – LWOFF (22) ,Institut Pasteur, Paris


Le Hub Bioinformatique et Biostatistique de l’Institut Pasteur organise des cours thématiques ouverts à tous. La première session intitulée « Analyse de données avec R » aura lieu tous les mardis matins, du 8 mars au 12 avril, en salle rétrovirus n°14, rez-de-chaussée du bâtiment Lwoff. Les cours seront donnés en Français et alterneront théorie et pratique avec RStudio. Il est demandé à chaque participant de venir avec un ordinateur portable chargé sur lequel il aura préalablement installé les éléments nécessaires (R, Rstudio et les fichiers de données sur lesquels nous travaillerons). La liste complète des fichiers et logiciels nécessaires sera disponible sur la page web du cours une dizaine de jours avant le début de la session.

Ce cours est une initiation à l’analyse de données. Il est préférable d’avoir une connaissance minimale de R. Dans le cas contraire, un tutoriel d’initiation est disponible sur la page web du cours et les notions de base de R seront rappelées pendant la pratique. Pour les personnes n’ayant jamais utilisé R, il peut être utile d’avoir des connaissances de base en programmation, quel que soit le langage. Le cours s’adresse à des personnes qui veulent apprendre ou ré-apprendre à utiliser les statistiques à bon escient pour leurs propres projets. L’objectif est de présenter et expliquer les principales notions de statistiques utiles pour décrire un jeu de données, en explorer les propriétés afin d’en tirer des conclusions robustes, utiliser à bon escient les méthodes les plus courantes (tests d’hypothèse, ACP, …) et savoir lire, interpréter (et éventuellement aborder d’un œil critique) les résultats présentés dans les publications. Nous utiliserons le moins possible le formalisme mathématique mais insisterons sur les propriétés des méthodes, leurs pré-requis, l’interprétation des résultats. Nous aborderons les notions d’analyse exploratoire, ACP, clustering, estimation, échantillonnage, régression, tests d’hypothèse, planification d’expérience. Les inscriptions sont maintenant fermées.
Installation requise:

Documents

Programme Support de cours Commandes R Jeux de données Evaluation

Programme Training_MorningSessions_Stat

Supports de cours

Intro R :

Training_MorningSessions_Stat_IntroR

Session 1 : statsSessionLecture1 Session 2 : statsSessionLecture2

Session 3 : Session3_MultivariateAnalaysis Session 4: statisticalLawsCourse expDesigns Session 5 et 6: Stat_Session5_6

Commandes R

CommandesSession1.R CommandesSession3.R CommandesSession4.R CommandesSession5.R CommandesInternal.R

Jeux de données

LungA LungB LungC Session3_dat_pca_clus Session4_exprs Session5-6

Evaluation

Sorry. This form is no longer available.

Training – Session d’hiver : programmation et scripting – 11 February 2016

EVENT : C3BI Training – Programmation & Scripting

Ecole Du C3BI : Session d’hiver : programmation et scripting


From : 11/02/2015

To : 25/02/2015


Objectif de la formation : Ce cours s’adresse à toute personne du campus souhaitant acquérir des bases de la programmation et du scripting utiles à la bioinformatique et ayant du mal à trouver du temps pour se former tout le long de l’année.
Pré-requis :Aptitude à travailler onze jours en continu en informatique et avoir des besoins confirmés par des projets en cours ou à venir.

Cette formation n’est accessible qu’aux personnes de l’Institut Pasteur, retrouvez les modalités d’inscription sur le site intranet de Pasteur.

Trainings – Leishield Training Course on Next Generation Sequencing

EVENT : C3BI Training – NGS Data Analysis

Leishield – Training Course on Next Generation Sequencing


Organizing Committee & Module coordinators : Fatma Z. Guerfali, Antonio V. Borderia,  Marie-Agnès Dillies, Christophe Malabat, from Institut Pasteur Tunis & C3BI

Date : from 30/11/2015 to 04/12/2015

Location : Pacific room – CIS (22), Institut Pasteur, Paris


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.

CoursLeishield

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.

 
LeiSHield_NGS_WORKSHOP

C3BI Training – – Introduction à la phylogénie moléculaire

Upcoming Events : C3BI Training – Phylogeny – 29/09/2015 at 09:30 am in Retrovirus room

Date : 29/09/2015 at 09:30 am Location : Retrovirus (Lwoff) Speakers/Trainers : , from C3BI For any questions, suggestions (or to volunteer) for future talks/trainings or general feedback please contact us at c3bi-ask@pasteur.fr

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) Website : more details

C3BI