Curriculum vitae

Short introduction

I am a support data scientist at the University of Amsterdam (Swammerdam Institute for Life Sciences) helping fellow researchers on Research Data Management and Data Analysis. On a daily basis, I work mostly with Plant Scientists that are struggling with various (plant) genomics and other “omics” issues. I also participate in a pilot project at the University of Amsterdam to implement the iRODS Open Source Data Management Software together with a graphical use interface called “YODA” developed by the University of Utrecht.
To reach out to more scientists and gather a community of computational life scientists, I also coordinate a Mozilla Study Group called the “Amsterdam Science Park Study Group”.

Research experience

  • Jan 2019 - Present: Data scientist & Data Manager - University of Amsterdam, Swammerdam Institute for Life Sciences (The Netherlands)
  • May 2014 - May 2018: Postdoctoral fellow - University of Amsterdam, Swammerdam Institute for Life Sciences (The Netherlands)
  • May 2010 - May 2014: Postdoctoral fellow - Jean-Pierre Bourgin Institute (Versailles, France)
  • October 2006 - December 2009: PhD in Plant Molecular Biology - University of Montpellier (France)

Education

Expertise

  • Scientific programming in Python:
    • Data import and transformation with Pandas.
    • Machine Learning in Python with scikit-learn.
    • Basic image processing with Pillow and scikit-image.
    • bioinformatics using mostly Biopython for fasta/fastq sequence parsing and pipeline development with Snakemake.
  • Version control: daily user of git and Github.
  • Data analysis in R:
    • data transformation and visualisation with tidyverse.
    • exploratory data analysis: PCA, heatmaps, plots.
    • unsupervised analysis: PCA, clustering.
    • linear, generalised and regularised regressions. (elastic net).
    • survival analysis (survminer)

Training and support activities

Carpentries workshop

2019-01-14/15: Software Carpentry workshop in Amsterdam. Co-organizer (together with Like Fokkens) and teacher (Shell basics and Git/Github). 24 attendees. Website link. 2019-02-05/06: Data Carpentry Genomics workshop in Wageningen. Teacher (Variant Calling). 35 attendees. 2017-12-12/13: Data Carpentry Genomics workshop in Amsterdam. Co-organizer and teaching. 26 attendees.

Community building and guidance

Since 2017, I coordinate a small group of biologists willing to make progress in scientific programming (data visualisation, genomics, statistics, etc.). It is called “Amsterdam Science Park Study Group” and is officially linked to the Mozilla Science Lab organisation. I make sure that regular one-hour sessions take place (every two weeks) and participate in lesson development. Sessions can also be longer (afternoons) to dive further into a topic of interest. Furthermore, I regularly organise two-day Carpentries Foundation workshop as part of the Amsterdam Study Group activities.
More info here on the Study Group website.

Workshop animation

PDF version