George Marchment
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George Marchment
george.marchment[at]universite-paris-saclay.fr

PhD Student
Université Paris-Saclay
LISN Laboraty

About


I am a 3rd year PhD student at Université Paris-Saclay. My research interests include data science, graph algorithms and bioinformatics.

PhD Candidate

A graph-based framework for scientific workflows: modelling, abstraction, and visualisation for reuse

Supervisors

Summary

Over the past two decades, scientific workflows have become the preferred way to develop scientific analyses. In particular, they are designed to define highly reproducible analyses, while facilitating their development, execution, sharing and reuse. Recently, workflow systems like Nextflow and Snakemake have emerged as valuable tools for bioinformaticians with programming expertise. These systems offer flexible scripting languages that enable swift development and execution, enhancing their usability. Therefore, a growing number of workflows are available on online platforms such as GitHub and GitLab; these workflows can be heterogeneous and complex, thus hard to gain understanding. To improve reuse of scientific workflows, this PhD thesis proposes a framework to gain insight into them efficiently. To achieve this, the following tasks should be considered. (1) Describe workflows in a homogeneous graph-based way. (2) Bridge the gap between heterogeneous source code and homogeneous workflow graphs. (3) Define a manner to automatically simplify the workflow graphs, using elements inherently defined in the workflow. (4) Design a module capable of viewing the simplified graph at different simplification levels, using a visual standard already familiar to developers and linking the workflow logic to this visualisation.

Diplomas

  • Master's Degree in Bioinformatics, Computational Biology Track
    Digicosme scholarship for excellence
    Université Paris-Saclay | 2021-2023

  • Double Bachelor's Degree in Mathematics and Computer Science
    Université Paris-Saclay | 2018-2021

Publications

  • George Marchment, Sarah Cohen-Boulakia, Alain Denise and Frédéric Lemoine. Workflow abstractions for automatic modularity: improving workflow code reusability. Future Generation Computer Systems, September 2026. (Accepted: waiting to be published)

  • Lénora Buggenhoudt, George Marchment, Anne-Flore Cabouat, Frédéric Lemoine, Caroline Appert, and Sarah Cohen-Boulakia. MetroFlow: Visualizing Bioinformatics Workflow Source Code as Interactive Metro-Maps. IEEE Working Conference on Software Visualization (VISSOFT), September 2026.

  • Marie Schmit, Ulysse Le Clanche, George Marchment, Sarah Cohen- Boulakia, Olivier Dameron, Alban Gaignard, Frédéric Lemoine, and Hervé Ménager. A Standards-Based Knowledge Graph that Bridges Scientific Workflows, Run-Time Provenance, and Tool Registries. Semantic Web Applications and Tools for Health Care and Life Sciences, March 2026. https://hal.science/hal-05517640/

  • George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, and Sarah Cohen-Boulakia. BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization. NAR Genomics and Bioinformatics, 6(3):lqae092, Sept. 2024. https://doi.org/10.1093/nargab/lqae092

  • Marine Djaffardjy, George Marchment, Clémence Sebe, Raphael Blanchet, Khalid Belhajjame, Alban Gaignard, Frédéric Lemoine, and Sarah Cohen-Boulakia. Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems. Computational and Structural Biotechnology Journal, 21:2075–2085, Jan. 2023. https://doi.org/10.1016/j.csbj.2023.03.003

Book chapters

  • Sarah Cohen-Boulakia, Frédéric Lemoine, George Marchment, Marine Djaffardjy, Alban Gaignard, Clémence Sebe, and Khalid Belhajjame. Reuse and Reproduce Bioinformatic Pipelines using Scientific Workflow Systems. In Berlin Universities Publishing, editor, Workflow systems for large-scale scientific data analysis. Berlin Universities Publishing, 2026. https://pasteur.hal.science/pasteur-05640482/

  • Sarah Cohen-Boulakia, George Marchment, Thomas Cokelaer and Frédéric Lemoine. Reprohackathons: Training efforts to increase Bioinformatics Reproducibility using Scientific Workflow systems. In Berlin Universities Publishing, editor, Workflow systems for large-scale scientific data analysis. Berlin Universities Publishing, 2026. https://pasteur.hal.science/pasteur-05640478v1

Posters

  • George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, and Sarah Cohen-Boulakia. (2024) BioFlow-Insight: Leveraging Graph representations to Facilitate the Reuse of Bioinformatics Workflows. Poster presented at the ACM REP Conference, Rennes, France. https://gitlab.liris.cnrs.fr/sharefair/posters/acm-rep-2024/-/blob/main/Poster%20ACM%20REP.pdf?ref_type=heads

  • George Marchment, Marie Schmit, Clémence Sebe, Frédéric Lemoine, Hervé Ménager, and Sarah Cohen-Boulakia. (2024) Representing bioinformatics Nextflow workflows in RO-Crate: challenges and opportunities. Poster presented at the Semantic Web Applications and Tools for Health Care and Life Science Conference, Leiden, The Netherlands. https://hal.science/hal-04540040

Talks

  • MetroFlow: automatic, interactive metro‑map visualisation for enhancing transparency and comprehensibility of Nextflow workflows
    JOBIM | 2026

  • MetroFlow: Generating Interactive Metro-Maps from Workflow Code
    Nextflow Summit | 2025 | Link to talk

  • BioFlow-Insight: Leveraging Graph representations to Facilitate the Reuse of Bioinformatics Workflows.
    ACM REP | 2024

Tutorials Given

  • Computational Reproducibility With Scientific Workflows: Analysing viral genomes with Nextflow
    ACM REP | 2025 | Link to tutorial

Projects