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In this paper we settle a logical semantics for the class CC of concurrent constraint programming languages and for its extension LCC based on linear constraint systems. Besides the characterization in intuitionistic logic of the stores of CC computations, we show that both the stores and the successes of LCC computations can be characterized in(More)
We introduce a formalism to represent and analyze protein-protein and protein-DNA interaction networks. We illustrate the expressivity of this language, by proposing a formal counterpart of Kohn's compilation on the mammalian cell cycle control. This effectively turns an otherwise static knowledge into a discrete transition system incorporating a(More)
In this article we present the Biochemical Abstract Machine BIOCHAM and advocate its use as a formal modeling environment for networks biology. Biocham provides a precise semantics to biomolecular interaction maps. Based on this formal semantics, the Biocham system offers automated reasoning tools for querying the temporal properties of the system under all(More)
We study a new fixpoint semantics for logic programs with negation. Our construction is intermediate between Van Gelder’s well-founded model and Gelfond and Lifschitz’s stable model semantics. We show first that the stable models of a logic programP are exactly the well-supported models ofP, i.e. the supported models with loop-free finite justifications.(More)
We propose a generic type system for the Constraint Handling Rules (CHR), a rewriting rule language for implementing constraint solvers. CHR being a high-level extension of a host language, such as Pro-log or Java, this type system is parameterized by the type system of the host language. We show the consistency of the type system for CHR w.r.t. its(More)
Finding mathematical models satisfying a specification built from the formalization of biological experiments, is a common task of the modeller that techniques like model-checking help solving, in the qualitative but also in the quantitative case. In this article we propose to go one step further by defining a continuous degree of satisfaction of a temporal(More)
Temporal logics and model-checking techniques have proved successful to respectively express biological properties of complex biochemical systems, and automatically verify their satisfaction in both qualitative and quantitative models. In this paper, we propose a finite time horizon model-checking algorithm for the existential fragment of LTL with numerical(More)