Thomas's necessary conditions for the existence of multiple steady states in gene networks have been proved by Soulé with high generality for dynamical systems defined by …
BIOCHAM-4 is a tool for modeling, analyzing and synthesizing biochemical reaction networks with respect to some formal, yet possibly imprecise, specification of their behavior. We …
Automating the process of model building from experimental data is a very desirable goal to palliate the lack of modellers for many applications. However, despite the spectacular …
Experimental observations have put in evidence autonomous self-sustained circadian oscillators in most mammalian cells, and proved the existence of molecular links between the …
In recent years Systems Biology has become a rich field of study, trying to encompass all the information that has become available thanks to the new high-throughput techniques of …
Experimental observations have put in evidence autonomous self-sustained circadian oscillators in most mammalian cells, and proved the existence of molecular links between the …
In Systems Biology, modelers develop more and more reaction-based models to describe the mechanistic biochemical reactions underlying cell processes. They may also work, however, …
Experimental observations have put in evidence autonomous self-sustained circadian oscillators in most mammalian cells, and proved the existence of molecular links between the …
In Mathematical Biology, many dynamical models of biochemical reaction systems are presented with Ordinary Differential Equations (ODE). Once kinetic parameter values are fixed, …
Constraint programming is traditionally viewed as the combination of two components: a constraint model and a search procedure. In this paper we show that tree search procedures …
Model reduction is a central topic in systems biology and dynamical systems theory, for reducing the complexity of detailed models, finding important parameters, and developing …
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In this paper we study the problem of deciding the existence of a subgraph epimorphism between two graphs. Our interest in this variant of graph matching problem stems from the …
Biochemical reaction networks grow bigger and bigger, fed by the high-throughput data provided by biologists and bred in open repositories of models allowing merging and …
In this work, we compare CLP and SAT solvers on the NP-complete problem of deciding the existence of a subgraph epimorphism between two graphs. Our interest in this variant of …
Models of biochemical systems presented as a set of formal reaction rules with kinetic expressions can be interpreted with different semantics: as either deterministic Ordinary …
Model reduction is a central topic in systems biology and dynamical systems theory, for reducing the complexity of detailed models, finding important parameters, and developing …
Background We present a way to compute the minimal semi-positive invariants of a Petri net representing a biological reaction system, as resolution of a Constraint Satisfaction …