🔝

👋 Hej! I am:

  • 🧑‍🎓 a PhD in computational biology
    I was working in CRAN/LORIA in the capsid team, supervised by Taha Boukhobza & Malika Smail-Tabbone;
  • 💼 currently visiting the computer science department of the university of Iowa. I continue working on the formal analysis of Boolean networks and reaction networks;
  • 🌍 a nancéienne (🇫🇷), ex-lilloise (🇫🇷), ex-parisienne (🇫🇷), happy to move abroad;
  • 🐍 a Python lover (the programming language), also fond of Answer-Set Programming (ASP), but not much of R;
  • 🐀 a rat care-taker (the cute animal);
  • 🎸🎺 a musician (guitar and trumpet);

You may want:

  • 📧 my e-mail address: athenais DOT vaginay AT loria DOT fr;
  • 📰 my academic papers on HAL / Google scholar / dblp
    (/!\ dblp covers publications from computer science only) ;
  • linkedin-logo my LinkedIn (updated in August 2023);
  • github-logo my GitHub
    (the code for my PhD research is stored on the private GitLab github-logo of my lab. It is accessible on request);
  • 📭 my work address (I love letters!):
    Bureau B142
    Campus Scientifique, 615 Rue du Jardin-Botanique
    54506 Vandœuvre-lès-Nancy

Feel free to get in touch with me (in french or english). :)

💬 Talks

The list below should be more or less exhaustive. The slides are available for most of the presentations.
List

Constraint-based abstraction of reaction networks to Boolean networks

5th December 2023
At GT CODAG , GREYC, Caen, France.
Slides
Abstract Reaction networks and Boolean networks are two prominent approaches for modeling biological systems. They rely on drastically different philosophies : the former consists of a detailed process-centred description with continuous time and values and the latter of an abstract species-centred description with discrete steps and Boolean values.
In order to better understand the relationship between these two formalisms, my PhD work focused on converting reaction networks to Boolean networks. This presentation delves into the pivotal role of constraints during the two steps of the process: (1) in the definition of the properties of the input reaction network we want to preserve and (2) the synthesis of the Boolean networks complying with these properties.
So far, the evaluation of the approach on toy examples and real-world reaction networks from the repository BioModels, has demonstrated its effectiveness. The perspectives mainly concern the practical relevance of the Boolean networks we synthesise, as well as the formal exploration of the relationship with other semantics of reaction networks.

From reaction networks to Boolean networks: why and how

14 November 2023
At CANA seminar, LIS, Marseille, France.
Slides
Abstract One way to get new insights about complex biological systems is to convert between modelling formalisms. Here, we deal with the conversion of reaction networks interpreted with the differential semantics, into Boolean networks. The conversion is particularly challenging, as it requires a drastic change in perspective: from a process-centred description with continuous time and values to a species-centred description with discrete steps and Boolean values. The conversion I present here is based on my PhD work. It aims at preserving properties from the input reaction network, such as its structure (the direct influences between the components) and its binarised transient dynamics (the transitions between the Boolean configurations). We will see how to extract the structure and dynamics of a reaction network, and how to use answer-set programming synthesise complying Boolean networks. So far, the evaluation of the approach on toy examples and real-world reaction networks from the repository BioModels, has demonstrated it effectiveness in synthesising Boolean networks complying with the input reaction networks. It also paved the way of the formal study of the relationship between the differential semantics of reaction network and Boolean networks. The perspectives mainly concern the practical relevance of the Boolean networks we synthesise, as well as the formal exploration of the relationship with other semantics of reaction networks.

Synthesis of Boolean Networks from the Structure and Dynamics of Reaction Networks

7th July 2023
At Loria, Nancy, France (PhD defense).

Sélection et analyse de modèles pour les réseaux biologiques

13th December 2022
At FCH seminar, Nancy, France (invited presentation).

Systems biology, reaction and Boolean networks: introduction and conversion from reaction network to Boolean networks

27th August 2022
At Vino (summer school / reading group), Campo Tures, Italy.

Differential Equations and differential invariants

22th August 2022
At Vino (summer school / reading group), Campo Tures, Italy (book chapter presentation).

Modelling Biological Systems with Boolean Networks

18th Nov 2021
At FCH' scientific day, Nancy, France (invited presentation).

SBML2BN: an Integrative Pipeline for the Synthesis of Boolean Networks from SBML Models

23rd Septembre 2021
At CMSB'21, Bordeaux, France (poster flash).

ASKeD-BN: Automatic Synthesis of Boolean Networks from Knowledge and Data

23th Jun. 2021
At OLA'21, online (paper presentation). Conference paper

Towards an automatic conversion from SBML core to SBML qual

30 Jul. 2019
At JeBiF'21 @ JOBIM, Nantes, France (flash poster presentation)

Quick Presentation

04 Apr. 2019
Loria Departement D5' day, Nancy, France

caspid "tea-time" seminars

Those are monthly scheduled seminars of the capsid team During my PhD, the talks below have mostly been used to keep my team updated about my work, and to rehearse presentations for conferences and other seminars. This is why I keep the list separated from the other talks.
List

ASKeD-BN: Automatic Synthesis of Boolean Networks from Knowledge and Data (OLA rehearsal)

Jun. 2021
caspid "tea-time" seminar, Nancy, France

Constrained Enumeration of Boolean Networks from Biological Data and Knowledge (prepare OLA submission)

19 Jan. 2021
caspid "tea-time" seminar, Nancy, France
Slides

The Search Space of the Logical Function Synthesis Problem — Application for Biological Systems

26 May 2020
caspid "tea-time" seminar, Nancy, France
Slides

Automatic Transformation from Reaction Models to Boolean Models Using Answer-Sets Constrained by a Topology and an Abstracted Dynamic

23 Jan. 2020
caspid "tea-time" seminar, Nancy, France
Slides

What I've learn this summer: recap Bioregul summer school (Porquerolle) and JeBIF + JOBIM (Nantes)

30 Jul. 2019
caspid "tea-time" seminar, Nancy, France

Introduction to Critical Thinking (in french)

12 Feb. 2019
caspid "tea-time" seminar, Nancy, France
Slides

Presentation of my Thesis Project

28 Nov. 2018
caspid "tea-time" seminar, Nancy, France

📄 Publications

I put my papers on HAL.

👩‍🏫 Teaching

The class links items are for the students to whom I gave the class (they require connexion on the uni website), but do not hesitate to reach out if you want to know more about it.
List
  • 2021-2022 (IDMC - L1 MIASH -- Anne Boyer)
    Algorithmique et structure de données (semestre 1)
    Arche
  • 2021-2022 (IDMC - L1 MIASH -- Laurent Vigneron)
    Programmation C (semestre 1)
  • 2021-2022 (IDMC - L1 MIASH -- Armelle Brun)
    Programmation C (semestre 2)
    Arche
  • 2021-2022 (IDMC - L2 MIASH -- Maxime Amblard)
    Traitement automatique des langues (semestre 2)
    Arche
  • 2021-2022 (IDMC - M1 SC, SDL, TAL -- Mathieu d'Aquin)
    Programmation Python (semestre 1)
    Arche
  • 2021-2022 (IDMC - M2 TAL et SC)
    Méthodologie, LaTeX et gestion de bibliographie
    Arche
  • 2021-2022 (IDMC - M1 TAL et SC)
    LaTeX et gestion de bibliographie
    Arche
  • 2019-2020 (IUT Brabois - DUT GBS 1A -- Alexandre Desforges)
    Bureautique et recherche documentaire -- Outils informatiques (semestre 1)
    Arche
  • 2019-2020 (IUT Brabois - DUT GB2A 1A -- Damien Cornu)
    Bureautique -- Informatique-Word-Powerpoint (semestre 1)
    Arche
  • 2016-2017 (Univ. Paris Diderot - L1 EA)
    Bureautique, vie numérique et recherche documentaire -- Outils pour la Bureautique et internet (semestre 2)
    Moodle
  • 2014–2015 (Univ. Paris Diderot - tutorat L1)
    Bureautique, vie numérique et recherche documentaire -- Outils pour la Bureautique et internet