Sylvain Soliman

Reifying Global Constraints

Global constraints were introduced two decades ago as a means to model some core aspects of combinatorial problems with one single constraint for which an efficient domain …

Inferring Reaction Models from ODEs

A Boolean Model for Enumerating Minimal Siphons and Traps in Petri Nets

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

Petri-nets are a simple formalism for modeling concurrent computation. Recently, they have emerged as a powerful tool for the modeling and analysis of biochemical reaction …

Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures

Finding mathematical models satisfying a specification built from the formalization of biological experiments, is a common task of the modeler that techniques like model-checking …

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

In systems biology, the number of available models of cellular processes increases rapidly, but re-using models in different contexts or for different questions remains a …

Steady-state Solution of Biochemical Systems, Beyond S-systems via T-invariants

A Unique Transformation from Ordinary Differential Equations to Reaction Networks

SBGN support in BIOCHAM

A graphical method for reducing and relating models in systems biology

Motivation: In Systems Biology, an increasing collection of models of various biological processes is currently developed and made available in publicly accessible repositories, …

On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle

In systems biology, the number of models of cellular processes increases rapidly, but re-using models in different contexts or for different questions remains a challenging issue. …

Model-based Predictions of the Influence of Circadian Clock Genes Knock-Outs on the Cell Cycle

The existence of links between the cell division cycle and the circadian clock has been recently discovered. In this research report, we perform a small in silico analysis of how …

Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans

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

Systems biologists build models of bio-molecular processes from knowledge acquired both at the gene and protein levels, and at the phenotype level through experiments done in …

On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology

Abstract interpretation and types for systems biology

Abstract interpretation is a theory of abstraction that has been introduced for the analysis of programs. In particular, it has proved useful for organizing the multiple semantics …