Making a good resume

The resume is the first thing the recruiter will read about you. I revised my resume multiple times already and continue to sharpen it. Here I describe the structure and overall basics tips to make a competitive resume.

  • tech 

A global ocean atlas of eukaryotic genes

Single-celled microeukaryotes and small multicellular zooplankton account for most of the planktonic biomass in the world’s ocean. Seawater samples were collected from the global ocean during the Tara Oceans expedition to generate a global ocean reference catalog of genes from planktonic eukaryotes sampled RNA and to explore the expression patterns of community at different microscopic scales with respect to biogeography and environmental conditions.

OBITools: processing DNA metabarcoding data

The OBITools software is a set of tools specifically designed for processing Next Generation Sequencing data in a DNA metabarcoding context, taking into account taxonomic information.

Global determinants of fish genetic diversity

At the beginning of 2020, our team* has published the first global map of the genetic diversity of marine and freshwater fishes. This is an important instrument for the preservation of species. This first map is published in the journal Nature Communications. As I have done all the bioinformatics analysis, I thought I could present this work from my point of view as a computer scientist. Indeed, this work required the collaboration of a wide range of professions: ecologist, oceanographer, statistician and geneticist.


  • omics 

Team working with git

I've been using git for years, alone or in collaboration with my team. Over time, I developed habits that I present in this article.

  • tech 

Landscape genomics

Environmental conservation issues have urged a need to better understand and describe species and populations on Earth. Recently, progress in sequencing technologies made it possible to refine this understanding through genomics. Understanding and describing populations of living organisms in a given environment by exploiting sequencing data is the ultimate goal of landscape genomics. So this article is an introduction of this field.

Disk management on linux

In this article, I resume some bash commands to check up or manage partitions on a linux system. The commands would check what partitions there are on each disk and other details like the total size, used up space and file system etc.

  • tech 

Step-by-Step Guide to Creating R packages

In R, the fundamental unit of shareable code is the package. A package bundles together code, data, documentation, and tests, and is easy to share with others.

  • tech 


One of the most promising genetic techniques for improving biodiversity assessments is the metabarcoding of environmental DNA (eDNA). I did a state of the Art of available methods and developed serveral workflows to process and manage metabarcoding data from the Monaco Marine Scientific Exploration.

  • omics 

Linux System Administration Basics

Since Linux is a multi-user operating system, several people may be logged in and actively working on a given machine at the same time. Security-wise, it is never a good idea to allow users to share the credentials of the same account. In fact, best practices dictate the use of as many user accounts as people needing access to the machine.

  • tech 

Virtual environments, containers and scientific reproducibility

Containers provide an easy-to-use, secure, and reproducible environment for scientists to transport their studies between computational resources. As more communities are using Docker or Singularity, we enter into the age of high reproducibility or at least replicability so that the use of containers is mandatory for any study.

SGE user commands

Using a cluster environment is similar to using linux environments for your job submission. The difference is that you need to specify needed resources beforehand. The cluster is controlled by a SGE (Sun Grid Engine Software) that organizes the queues and resources. This sort of scheduling system is necessary when limited computational resources are shared by many. Here I show how to use Sun Grid Engine for job submission, monitoring and troubleshooting.

  • tech 

A little introduction to BASH (Born Again Shell)

This is some hints about shell script programming based on examples. I provide here some little scripts which will hopefully help to understand the very basics.

  • tech