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About

The Bioinformatics and Biostatistics Hub is a team of research engineers lead By Marie-Agnès Dillies and Christophe Malabat and dedicated to bring support in computational biology to Institut Pasteur’s research Units and platforms. The Hub is organized around seven expert groups :

Hub also has expertise outside of these expert groups like:

The above list of expertise is not exhaustive. Do not hesitate to visit the Groups web pages or contact the Hub director if you don’t find the one you need. The Hub can help Institut Pasteur’s scientists in many ways:

  • By direct interaction during the open-desk sessions. Every Tuesday morning (now on Teams)
  • By answering short questions submitted through our web site (link here)
  • By collaborating to research projects. The Hub support is:
    • Free of charge for projects lasting less than 3 months of effective working time – short projects
    • Half of the full salary of an Engineer for projects of 4 months or more – long projects

In any case projects must be submitted on our website with as much detail as possible. Submit a project All short projects are accepted if the required expertise is available in the Hub within a reasonable time. Long projects are examined by the Hub executive steering committee who meets three times a year. A specific template is available for long projects and has to be sent to Marie-Agnes Dillies and Christophe Malabat two weeks before the steering committee meeting. Some discussions and exchanges with the Hub are encouraged before submitting long projects. A detachment of an Hub engineer is also possible for very long projects. See the detached section for more information. These different possibilities are summarized in the table below:

Type Cost Description decision process
Long project
  • Half of the charged salary
  • about 3k€/month
  • 1.5 k/month for strategic projects
  • no HR affiliation
  • not included into ETM
  • Half the cost of a post-doc
  • Duration adapted to the project
  • no hiring
Validated by Executive steering committee after reviewing request using this template
Detachment
  • Included into the Unit package
  • HR affiliation
  • Included into ETM
  • from 2 to 5 years, renewable
  • Hiring or internal mobility
Validated by IP’s Direction and Executive steering committee
Detachment on Grant
  • 80% of the salary
  • on external grant, typically ERC
  • HR affiliation
  • Included into ETM f
  • rom 2 to 5 years, renewable
  • Hiring or internal mobility
Validated by IP’s Direction and Executive steering committee

The Hub is also involved in two other activities:

  • Software development: Hub engineers have developed many tools to help data analyses such as Shaman, JASS. More details in the software section
  • Teaching and training: Hub engineers are deeply involved into sharing their knowledge with PhD students, post-docs or permanent scientists from IP in Paris and in the RIIP. More information in the courses section

Services

Open Desk of the Hub of Bioinformatics and Biostatistics

Every week, on Tuesday mornings, from 10 to 12, Hub engineers are enlisted to provide a direct support to any members of Institut Pasteur seeking for help on bioinformatics or biostatistics related subjects. Hub […]

Software

Members

Groups

Former Members

Courses

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

Ce cours a pour objectif de donner les bases théoriques et pratiques, ainsi que les bonnes pratiques nécessaires au démarrage de travaux en phylogénie et épidémiologie moléculaires. Les sessions théoriques donneront les bases du […]

2019-10-07 09:30:00 2019-11-11 17:30:00 Europe/Paris Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation Ce cours a pour objectif de donner les bases théoriques et pratiques, ainsi que les bonnes pratiques nécessaires au démarrage de travaux en phylogénie et épidémiologie moléculaires. Les sessions théoriques donneront les bases du […] 28 Rue du Dr Roux, Paris, France

Introduction à l’analyse Bio-informatique de séquences

L’objectif de cette formation est de présenter, au travers de l’utilisation d’outils largement utilisés, quelques grands principes sur l’analyse de séquence. L’ensemble de la formation combine exposés théoriques (fondements méthodologiques des programmes) et applications […]

2019-09-23 09:00:00 2019-09-27 17:00:00 Europe/Paris Introduction à l’analyse Bio-informatique de séquences L’objectif de cette formation est de présenter, au travers de l’utilisation d’outils largement utilisés, quelques grands principes sur l’analyse de séquence. L’ensemble de la formation combine exposés théoriques (fondements méthodologiques des programmes) et applications […] Institut Pasteur, Rue du Docteur Roux, Paris, France

High Throughput Sequencing Data Analysis on Genomics, Metagenomics and Transcriptomics

The National Center for Aquaculture and Marine Research (CENAIM) of the Polytechnic School of the Litoral (Ecuador), the Computational Biology and Microbial Ecology Group (BCEM) of the Universidad de los Andes (Colombia) and the […]

2018-09-13 09:00:00 2018-09-21 17:00:00 Europe/Paris High Throughput Sequencing Data Analysis on Genomics, Metagenomics and Transcriptomics The National Center for Aquaculture and Marine Research (CENAIM) of the Polytechnic School of the Litoral (Ecuador), the Computational Biology and Microbial Ecology Group (BCEM) of the Universidad de los Andes (Colombia) and the […] Escuela superior politécnica del litoral, Guayaquil, Ecuador

Introduction à la phylogénie moléculaire

Ce cours d’introduction à la phylogénie a pour objectif d’apporter les connaissances théoriques et les bonnes pratiques d’analyse de données par les logiciels de phylogénie. Il est ouvert aux formations doctorales et aux professionnels […]

2019-02-18 09:00:00 2019-02-22 17:00:00 Europe/Paris Introduction à la phylogénie moléculaire Ce cours d’introduction à la phylogénie a pour objectif d’apporter les connaissances théoriques et les bonnes pratiques d’analyse de données par les logiciels de phylogénie. Il est ouvert aux formations doctorales et aux professionnels […] 28 Rue du Dr Roux, Paris, France

From genes to function: a survival guide to web-based tools for microbiologists

Target Audience: PhD students, Post-doctoral fellows, Research Staff and PIs that work in any field related to microbiology that requires to understand or predict gene function. Summary: Methods to allow experimental scientists lacking computer […]

2019-06-17 08:30:00 2019-06-21 17:30:00 Europe/Paris From genes to function: a survival guide to web-based tools for microbiologists Target Audience: PhD students, Post-doctoral fellows, Research Staff and PIs that work in any field related to microbiology that requires to understand or predict gene function. Summary: Methods to allow experimental scientists lacking computer […] Institut Pasteur, Rue du Docteur Roux, Paris, France

Analyse de séquences

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 […]

2018-03-19 09:30:00 2018-09-23 17:00:00 Europe/Paris Analyse de séquences 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 […] Institut Pasteur, Rue du Docteur Roux, Paris, France

Scientific Programming in Python

The ever growing usage of high throughput technologies in Biology is revolutionizing the life sciences and profoundly changing its practices. Scripting languages are used on a daily basis in life science labs in order […]

2017-03-06 09:30:00 2017-03-18 17:00:00 Europe/Paris Scientific Programming in Python The ever growing usage of high throughput technologies in Biology is revolutionizing the life sciences and profoundly changing its practices. Scripting languages are used on a daily basis in life science labs in order […] 25 Rue du Dr Roux, 75015 Paris, France

Introduction to Python Programming

Python is often used to learn programming as it is very readable and easy to write. Python is a very popular language in bioinformatics where many programs and libraries are written in python. This […]

2018-06-04 09:30:00 2018-06-08 17:00:00 Europe/Paris Introduction to Python Programming Python is often used to learn programming as it is very readable and easy to write. Python is a very popular language in bioinformatics where many programs and libraries are written in python. This […] 25 Rue du Dr Roux, 75015 Paris, France

Morning session – Data analysis using R

This course is an introduction to data analysis. It is better to have a minimal knowledge of R. If not, an introductory tutorial is available on the course’s web page and the basics of […]

2016-03-08 09:00:00 2016-04-12 12:00:00 Europe/Paris Morning session – Data analysis using R This course is an introduction to data analysis. It is better to have a minimal knowledge of R. If not, an introductory tutorial is available on the course’s web page and the basics of […] 28 Rue du Docteur Roux, Paris, France

sincellTE

Single cell transcriptomics and Epigenomics: Theory and Practice This workshop focuses on the large-scale study of heterogeneity across individual cells from a genomic, transcriptomic and epigenomic point of view. New technological developments enable the […]

2018-06-17 18:00:00 2018-06-22 14:00:00 Europe/Paris sincellTE Single cell transcriptomics and Epigenomics: Theory and Practice This workshop focuses on the large-scale study of heterogeneity across individual cells from a genomic, transcriptomic and epigenomic point of view. New technological developments enable the […] Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France

C3BI Course: 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 […]

2018-10-22 08:00:00 2018-10-27 19:00:00 Europe/Paris C3BI Course: 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 […] HKU-Pasteur Research Pole HKJC Building for Interdisciplinary Research 5 Sassoon Road, Pokfulam, Hong Kong

Projects

Transversal Project

Tools

Fundings

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Detached

Les membres du Hub peuvent être détachés dans une autre unité ou Plateforme de l’IP.

Pour les Unités de recherche, le membre du Hub détaché sera compté comme faisant partie du personnel accordé par la Direction de l’IP aux Unités dans le cadre de leu package. En règle générale, un seul ingénieur est accordé dans les G5 par exemple.

Pour les Plateforme, une demande spécifique doit être adressée au comité de pilotage et à la Direction de l’IP.

Dans certains cas, un ingénieur peut être détaché si le salaire est pris en charge par l’unité d’accueil, à l’aide d’un financement externe. L’engagement doit être d’au moins 3 ans. Une demande doit être adressée au comité de pilotage et à la Direction de l’IP.

Dans tous les cas, les ingénieur·e·s seront détaché·e·s à 80% dans l’entité hôte et conserveront 20% d’activités dans le Hub, principalement pour participer des actions collaborative et aux enseignements.

Steering committee

Steering Committee

The Hub Steering committee is composed of representants of all scientific Department and Direction of Institut Pasteur.

This committee meets once a year for exchanging on Hub advances during the past year.

It is also the occasion for the Hub to have a direct feedback from department and to improve its support to the campus.

Executive steering committee

The executive steering committee is in charge of the validation of ressource allocation for long projects. It will focus mainly on the scientific content and perspective of the project. Also it will be garant for a fare share of ressources between research Units of Institut Pasteur.

The executive committee meets three time a year (spring, summer and autumn/winter).
Past meetings :
– December 4th, 2020
– April 8th, 2021

Next meeting:
-Late August 2021

The executive committee is composed of:
– Didier Mazel (president)
– Christophe d’Enfert
– Patrick Trieu-Cuot
– Marc Delarue
– Simmonetta Gribaldo
– Roberto Toro
– Claudine Médigue

 

Contact

Phone: +33 (0)1 44 38 93 72 Email: bionfo-ask@pasteur.fr Address 25-28 Rue du Docteur Roux 75015, Paris France