Hands-on microbiome data analysis: tools for understanding microbial communities in health and disease

EVENT : C3BI Training


Main speaker : Gregorio Iraola, from Institut Pasteur de Montevideo Date : 03-12-2018 at 09:00 am Location : Institut Pasteur de Montevideo


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.

 

TEACHERS

Institut Pasteur Montevideo

  • Chair: Gregorio Iraola
  • Pablo Fresia
  • Daniela Costa
  • Cecilia Salazar
  • Verónica Antelo
  • Ignacio Ferrés
  • Matias Giménez
Institut Pasteur Paris
  • Marie Lopez
  • Amine Ghozlane
  • Angèle Benard
    • INVITED SPEAKERS
      • Gianfranco Grompone, Discovery Microbiome, Nutrition & Health Science Lead, Lesaffre, France.
      • David Danko, Director of Bioinformatics, MetaSUB International Consortium, Weill Cornell Medicine, US
       

      DEADLINE APPLICATIONS October 19, 2018. Send your CV (one page) and letter of motivation to: antonio.borderia@pasteur.fr

      Flyer_Microbiome_health-course_Montevideo_2018  

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)

C3BI Courses: Introduction to Molecular Phylogenetics – Hong Kong 2018

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 14th Midnight (HK time). Use the link if you can’t see the embedded form: https://goo.gl/forms/rgYrUNrEz6rqgELP2)

Linking gene and function, comparative genomics tools for biologists

EVENT : C3BI Training


Main speaker : Valerie de Crecy-Lagard, from University of Florida · Department of Microbiology and Cell Science
Date : 25-06-2018 at 08:00 am
Location : Retrovirus room – LWOFF (22) ,Institut Pasteur, Paris

Students will need to bring their laptop.


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)


Target audience: PhD students in biological sciences with a strong focus on microbiology/biochemical applications.

Instructor: Prof. Valérie de Crécy-Lagard is an expert in comparative genomics. She has been using comparative genomic methods to link gene and function for over twenty years and has developed curriculum the teach integrative data mining tools at all levels.

Module organization

The training aims at enabling researchers and students to 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.

The course will last 5 days and uses a blend of lectures and hands-on application

• Module 1: Basic bioinformatics tools day 1, morning). This module is to bring everyone up to date on the basic tools that will be routinely used in the course. These will include data extraction from major biological databases such as NCBI and Uniprot, Blast, multiple alignments, accessing precomputed phylogenetic trees and genome browsers.

• Module 2: Linking genes to pathway and pathway to genes (day 1, afternoon):.This module will focus on pathway databases, metabolic reconstruction and models and how mapping a gene to a pathway or more generally to biological system can ground truth a functional annotation.

• Module 3: Non homology based association methods (day 2, morning). Physical clustering, phylogenetic distribution, comparing whole genomes, iTOL visualization tools

• Module 4: Paralogs a blessing and a curse (day 2, afternoon). This module will focus on the tools and strategy to disambiguate paralog families. This includes, Basic phylogenetic tree building, paralog separation tools, building and comparing logos

• Module 5: Regulatory based associations. (day 3, morning). This module focuses on identifying regulatory sites, predicting regulatory networks, mining transcriptome data, and generating heatmaps and Venn diagrams.

• Module 6: Beyond transcriptomics, mining other types of high throughput experimental data (day 3, afternoon).. This module focuses on mining other types of experimental data Phenotype/fitness, protein interaction and complexes, localization, metabolomics.

• Module 7: Putting it together in the MicroScope platform (day 4, all day). This module proposed by the CEA will cover some of the techniques discussed above using Microscope : http://www.genoscope.cns.fr/agc/microscope/home/index.php

• Module 8: Putting it together with student examples (day 5, all day).). The last day of class students will have the opportunity to work on a protein family of their choice with the help of the instructors.


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

Hands-on High throughput Sequencing course in Bogota with the collaboration of Institut Pasteur and UniAndes

Hands-on course on High Throughput Sequencing data analysis: Genomics, Transcriptomics, Epigenomics

About

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.
Please be aware that the workshop will be delivered both in Spanish and English.

Trainers

Programme

   
 
  • 08:00 – 8:30 Registration
  • 08:30 – 12:30
    • Presentation of the course
    • Introduction to HTS/NGS technologies (Illumina, PacBio, NanoPore, etc.) [T]
    • Basic stats/probability concepts: particularities of HTS/NGS sampling, underlying distributions, etc. [T]
  • 14:00 – 18:00
    • Quality analysis (error and bias of different technologies, quality metrics in sequencing, etc) [T/P]
    • Introduction to file formats (FASTA, FASTQ, SAM, BAM, BED, GFF …) [T/P]
 
  • 08:30 – 12:30
    • Alignment and mapping algorithms [T]
    • Mapping against a reference – Mapping for removal of contaminants [P]
  • 14:00 – 18:00
    • Assembly [T/P]
 
  • 08:30 – 12:30
    • Transcriptomics: Expression quantification, differential analysis, splice variant analysis [T/P]
  • 14:00 – 18:00
    • Epigenomics [T/P]: Quality control of IP enrichment, peak calling and introduction to differential analysis [T/P]
 
  • 08:30 – 12:30
    • Pathway analysis and functional analysis [T/P]
  • 14:00 – 18:00
    • Introduction to analysis in Galaxy
    • Visualization of data sets in the genome browser IGV
 

Registration

Registration is compulsory. Please proceed to the following link to complete your registration.

Location

Universidad de los Andes
Bogotá, Colombia
Carrera 1 #18A-12
https://uniandes.edu.co/en   Enregistrer

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-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

 

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.