After an initial degree in Biology, I started my professional career as a software developer. Following the completion of my software engineering degree at the CNAM, I joined the Institut Pasteur, where I initially worked in the “Software and Databases” group. I joined the Bioinformatics and Biostatistics Hub within the Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI) as a Research Engineer in 2017, where I lead the WINTER group.
Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including […]
ELIXIR bio.tools – Tools Interoperability and Service Registry
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 […]
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 […]
A personal database system for large scale quantitative results exploration (Cassandre, PTR 463)
Cassandre is a project of personal database system, integrating a “user-friendly” interface to manage and explore multiple sets of large-scale experimental results in biology. Large-scale experiments that generate quantitative data, such as changes in […]
JASS – Joint Analysis of (GWAS) Summary Statistics
JASS is a python package that handles the computation of the joint statistics over sets of selected GWAS results, and the interactive exploration of the results through a web interface. The generation of joint […]
MacSyFinder & MacSyView
Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include […]
Python-cwlgen is a python library for the generation of CWL programmatically. It supports the generation of CommandLineTool and DockerRequirement. The library works for both Python 2.7.12+ and 3.6.0.
We have recently developed tools to visualize the results of CRISPR screens and design novel guide RNA for use in bacteria. These tools are available at crispr.pasteur.fr .
This project aims at efficiently storing millions of unique molecular compounds along with some of their already calculated properties. The database named Chem-REST is able to deal with extensive sets of data: millions of […]
ToolDog – Tool Description Generator
ToolDog is a program that generates tool description from a tool entry from https://bio.tools.
In order to boost the identification of low-molecular-weight drugs on protein-protein interactions (PPI), it is essential to properly collect and annotate experimental data about successful examples. This provides the scientific community with the necessary […]
2019Community curation of bioinformatics software and data resources, Brief. Bioinformatics 2019 Oct;.
2019The bio.tools registry of software tools and data resources for the life sciences, Genome Biol. 2019 08;20(1):164.
2018A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it., JOSS 2018.
2018Recommendations for the packaging and containerizing of bioinformatics software, F1000Research 2018, 7(ELIXIR):742 .
2017Using bio.tools to generate and annotate workbench tool descriptions, F1000Research 2017, 6(ELIXIR):2074.
2017Galaxy@pasteur, Mareuil F, Doppelt-Azeroual O and Ménager H. A public Galaxy platform at Pasteur used as an execution engine for web services [version 1; not peer reviewed]. F1000Research 2017, 6:1030 (poster) (doi: 10.7490/f1000research.1114334.1) .
2017ReGaTE: Registration of Galaxy Tools in Elixir, Gigascience 2017 Jun;6(6):1-4.
2017Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities, Future Generation Computer Systems.
2016Using registries to integrate bioinformatics tools and services into workbench environments, International Journal on Software Tools for Technology Transfer 18 (6), 581-586.
2015BioShaDock: a community driven bioinformatics shared Docker-based tools registry, F1000Research 2015, 4:1443.
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