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About

ONGOING PROJECTS

Galaxy administration/Maintenance (https://galaxy.web.pasteur.fr)
Bioweb:  Future directory of bioinformatics resources at the Institut Pasteur
ELIXIR Registry

SKILLS

Galaxy:  administration, API/Bioblend expertise
Programming: Python,  Javascript, Lua, R,
Development tools: GIT, Subversion, Emacs
Database: NoSQL (couchdb), MySQL, PostgreSQL
Bioinformatics: Preprocessing NGS data, MED-SuMo, Protein surface comparison, Protein functional  annotation.

OTHER ACTIVITIES

C3BI seminars and meetings management
Involved in Galaxy France Working Group (IFB)

FORMER PROJECTS

MetaGenSense(https://metagensense.web.pasteur.fr)
Disco-Bac (https://disco-bac.web.pasteur.fr)

Courses

09:00
06
Jun 2016
Course

Workshop: Bacterial RNAseq

We propose a skills training for PhD students on Bacterial RNAseq experiments Using total RNAs, we will i) enrich the mRNAs by depleting the rRNAs ; ii) prepare and sequence cDNA library and iii) analyse […]
Pathogenesis of Bacterial Anaerobes
Biomics
Microbiology
Marc Monot
Isabelle Martin-Verstraete
Bruno Dupuy
Odile Sismeiro
Rachel Legendre
Fabien Mareuil
Olivia Doppelt-Azeroual
2016-06-06 09:00:00 2016-06-10 17:00:00 Europe/Paris Workshop: Bacterial RNAseq We propose a skills training for PhD students on Bacterial RNAseq experiments Using total RNAs, we will i) enrich the mRNAs by depleting the rRNAs ; ii) prepare and sequence cDNA library and iii) analyse […] 28 Rue du Docteur Roux, Paris, France
09:00
10
Oct 2016
Course

Training: analysis of the transcriptome by RNAseq

The Transcriptome and Epigenome platform of the Biomics pole is organizing a one week (October 10, 2016 – October 14, 2016) training session dedicated to the analysis of the transcriptome by RNAseq. It  is […]
Biomics
Genomes and Genetics
Odile Sismeiro
Jean-Yves Coppee
Marie-Agnès Dillies
Hugo Varet
Rachel Legendre
Olivia Doppelt-Azeroual
Fabien Mareuil
Natalia Pietrosemoli
2016-10-10 09:00:00 2016-10-14 17:00:00 Europe/Paris Training: analysis of the transcriptome by RNAseq The Transcriptome and Epigenome platform of the Biomics pole is organizing a one week (October 10, 2016 – October 14, 2016) training session dedicated to the analysis of the transcriptome by RNAseq. It  is […] 28 Rue du Docteur Roux, Paris, France

Projects

Project
Ongoing
4 Members

ELIXIR bio.tools – Tools Interoperability and Service Registry

Hervé Menager (PI)

The cornerstone of the ELIXIR Tools platform is the bio.tools ELIXIR Tools and Data Services Registry, a discovery portal for a wide range of key bioinformatics resources, which is developed through ELIXIR-EXCELERATE Work Package […]
Project
Completed
7 Members

NGPhylogeny.fr

Frédéric Lemoine (PI)

New Generation Phylogeny.fr: Refactoring Phylogeny.fr for innovative phylogenetic services Phylogeny.fr is one of the main server available today able to run phylogenetic analysis pipelines. In the context of scientific workflows, none of the workflow […]
Project
Ongoing
8 Members

Bioweb

Hervé Menager (PI)

Bioweb is a web portal to search and access the bioinformatics resources available at the Institut Pasteur. It provides an overview of the resources available in the central infrastructure, as well as features to identify […]
Project
Ongoing
5 Members

ReGaTE

Hervé Menager (PI)

ReGaTE is a software component enabling the automated publication of Galaxy tools and workflows into the ELIXIR Tools and Data Services Registry. This registry is a web portal for the exploration of bioinformatics resources, […]

CV

FORMER PROFESSIONAL EXPERIENCE:

2011 – 2012 : Bioinformatics Engineer at Institut Pasteur in the platform Genotyping of Pathogens and Public health (PF8)
2009 – 2011 : Project Manager at MEDIT SA
(MED-SuMo server management: new functionalities and sources maintenance, Scientific validation, Prototype implementation for PPI comparison with MED-SuMo)
2006 – 2009 : Genome Analysis and Molecular Modelling PhD. at MEDIT SA / Paris-Diderot Université.
Title: Implémentation d’une méthode de classification de surfaces d’interactions protéiques et optimisation et extension du logiciel MED-SuMo (6 publications).

EDUCATION:

2009 : Molecular Modelling/Bioinformatics PhD. MEDIT SA / Paris-Diderot University (Paris VII)
2005 : Master 2 recherche en Biologie-Informatique, Paris-Diderot University (Paris VII)
2004 : Licence et Maîtrise d’Informatique, Université UPMC (Paris VI)

Publications

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