inr_logo_rouge
  • Home
  • Publications
  • Projects
  • Teaching
  • Posts
  • Links
  • Contact
  • Publications
    • Graphical conditions for the existence, unicity and number of regular models
    • On BIOCHAM Symbolic Computation Pipeline for Compiling Mathematical Functions into Biochemistry
    • Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches
    • MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps
    • Scalable Enumeration of Trap Spaces in Boolean Networks via Answer Set Programming
    • Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding
    • Efficient Enumeration of Fixed Points in Complex Boolean Networks Using Answer Set Programming
    • Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts
    • A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint
    • Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: a Hybrid Modeling Approach
    • Minimal trap spaces of Logical models are maximal siphons of their Petri net encoding
    • Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
    • Symbolic Methods for Biological Networks D2.1 Report on Scalable Methods for Tropical Solutions (T1.2)
    • Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop
    • COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms
    • A Polynomialization Algorithm for Elementary Functions and ODEs, and their Compilation into Chemical Reaction Networks
    • Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs
    • Model learning to identify systemic regulators of the peripheral circadian clock
    • Graphical Conditions for Rate Independence in Chemical Reaction Networks
    • On the Complexity of Quadratization for Polynomial Differential Equations
    • SBML Level 3: an extensible format for the exchange and reuse of biological models
    • Automated inference of Boolean models from molecular interaction maps using CaSQ
    • On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics
    • A Statistical Unsupervised Learning Algorithm for Inferring Reaction Networks from Time Series Data
    • Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels
    • Influence Networks compared with Reaction Networks: Semantics, Expressivity and Attractors
    • Executable Disease Networks: Adding dynamics to molecular maps
    • On Robustness Computation and Optimization in BIOCHAM-4
    • Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data
    • Model-based Investigation of the Circadian Clock and Cell Cycle Coupling in Mouse Embryonic Fibroblasts: Prediction of RevErb-α Up-regulation During Mitosis
    • A structural perspective on the dynamics of biochemical systems
    • Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: Prediction of RevErb-α up-regulation during mitosis
    • Influence Systems vs Reaction Systems
    • On Enumerating Minimal Siphons in Petri nets using CLP and SAT solvers: Theoretical and Practical Complexity
    • Model-based Investigation of the Effect of the Cell Cycle on the Circadian Clock through Transcription Inhibition during Mitosis
    • Inferring reaction systems from ordinary differential equations
    • Search by Constraint Propagation
    • Hybrid Simulations of Heterogeneous Biochemical Models in SBML
    • A constraint solving approach to model reduction by tropical equilibration
    • Trace Simplifications preserving Temporal Logic Formulae with Case Study in a Coupled Model of the Cell Cycle and the Circadian Clock (Best Student Paper Prize)
    • On the subgraph Epimorphism Problem
    • A stronger necessary condition for the multistationarity of chemical reaction networks
    • A Constraint Solving Approach to Tropical Equilibration and Model Reduction
    • On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models
    • Solving Subgraph Epimorphism Problems using CLP and SAT
    • Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem
    • A Boolean Model for Enumerating Minimal Siphons and Traps in Petri Nets
    • Inferring Reaction Models from ODEs
    • Reifying Global Constraints
    • Automatic Curation of SBML Models based on their ODE Semantics
    • Un modèle booléen pour l'énumération des siphons et des pièges minimaux dans les réseaux de Petri
    • Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures
    • Design, optimization and predictions of a coupled model of the cell cycle, circadian clock, DNA repair system, irinotecan metabolism and exposure control under temporal logic constraints
    • A Unique Transformation from Ordinary Differential Equations to Reaction Networks
    • Steady-state Solution of Biochemical Systems, Beyond S-systems via T-invariants
    • SBGN support in BIOCHAM
    • A graphical method for reducing and relating models in systems biology
    • Modelling molecular networks: relationships between different formalisms and levels of details
    • Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans
    • Model-based Predictions of the Influence of Circadian Clock Genes Knock-Outs on the Cell Cycle
    • On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle
    • On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle
    • A general computational method for robustness analysis with applications to synthetic gene networks
    • Modelling Biochemical Reaction Networks with BIOCHAM Extracting Qualitative and Quantitative Information from the Structure
    • Model Revision from Temporal Logic Properties in Computational Systems Biology
    • On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology
    • Abstract interpretation and types for systems biology
    • Modelling of FSHR-induced signalling network
    • Formal Cell Biology in Biocham
    • From reaction models to influence graphs and back: a theorem
    • Closures and Modules Within Linear Logic Concurrent Constraint Programming
    • Langages formels dans la machine abstraite biochimique BIOCHAM
    • Proceedings of CSCLP 2007: Annual ERCIM Workshop on Constraint Solving and Constraint Logic Programming
    • Coupling the Cell cycle and the Circadian Cycle
    • Machine Learning Biochemical Networks from Temporal Logic Properties
    • On Internalizing Modules as Agents in Concurrent Constraint Programming
    • BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
    • A Machine Learning approach to Biochemical Reaction Rules Discovery
    • Learning Transition Rules from Temporal Logic Properties
    • Apprentissage de règles de réactions biochimiques à partir de propriétés en logique temporelle
    • Machine Learning Bio-molecular Interactions from Temporal Logic Properties
    • The Biochemical Abstract Machine BIOCHAM
    • CLPGUI: A Generic Graphical User Interface for Constraint Logic Programming
    • Modelling and Querying Interaction Networks in the Biochemical Abstract Machine BIOCHAM
    • La programmation par contraintes
    • Pi-calculus and LCC, a Space Odyssey
    • Concurrent constraint programming and linear logic
    • Linear Concurrent Constraint Programming: Operational and Phase Semantics
  • Posts
    • Trappist is a tool for computing minimal trap spaces of a Boolean model.
    • Inférence automatisée de modèles Booléens à partir de cartes d'interaction moléculaire en utilisant CaSQ
    • CaSQ: Celldesigner as Sbml-Qual
    • Prolog programming guidelines
    • Cyclic Dice Programming Project
    • Nicotine
    • Japanese Restaurants in Paris
    • Creating Prolog executables
  • Projects
    • ANR DIFFERENCE
    • COVID-19 Disease Map
    • ANR-DFG SYMBIONT

Trappist is a tool for computing minimal trap spaces of a Boolean model.

Thu, Nov 30, 2023 · 0 min read
Go to Project Site
Last updated on Thu, Nov 30, 2023
Logical Model Influence Graph Trap Spaces Answer Set Programming
Sylvain Soliman
Authors
Sylvain Soliman
Computer Science Researcher
My research interests include computational systems biology and constraint programming
Inférence automatisée de modèles Booléens à partir de cartes d'interaction moléculaire en utilisant CaSQ Mon, May 25, 2020 →

© 2025 Me. This work is licensed under CC BY NC SA 4.0