From reaction networks to Boolean networks: why and how
👋 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; - 💼 now looking for a post-doc in systems biology (formal modeling with 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) ; -
my LinkedIn (updated in August 2023);
-
my GitHub
(the code for my PhD research is stored on the private GitLabof 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
Synthesis of Boolean Networks from the Structure and Dynamics of Reaction Networks
Synthesis of Boolean Networks from the Structure and Dynamics of Reaction Networks
Sélection et analyse de modèles pour les réseaux biologiques
Systems biology, reaction and Boolean networks: introduction and conversion from reaction network to Boolean networks
Differential Equations and differential invariants
ASKeD-BN: Automatic Synthesis of Boolean Networks from Knowledge and Data
From Chemical Reaction Networks to Boolean Networks, Automatically
From Quantitative SBML to Boolean Network
Modelling Biological Systems with Boolean Networks
SBML2BN: an Integrative Pipeline for the Synthesis of Boolean Networks from SBML Models
ASKeD-BN: Automatic Synthesis of Boolean Networks from Knowledge and Data
ASKeD-BN: Automatic Synthesis of Boolean Networks from Knowledge and Data
Towards an automatic conversion from SBML core to SBML qual
Quick Presentation
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)
Constrained Enumeration of Boolean Networks from Biological Data and Knowledge (prepare OLA submission)
The Search Space of the Logical Function Synthesis Problem — Application for Biological Systems
Automatic Transformation from Reaction Models to Boolean Models Using Answer-Sets Constrained by a Topology and an Abstracted Dynamic
What I've learn this summer: recap Bioregul summer school (Porquerolle) and JeBIF + JOBIM (Nantes)
Introduction to Critical Thinking (in french)
Presentation of my Thesis Project
📄 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