Bigraphical models for protein and membrane interactions

We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules representing biologically admissible interactions. At the protein level, these bigraphic reactive systems correspond exactly to systems of kappa-calculus. Membrane-level interactions are represented by just two general rules, whose application can be triggered by protein-level interactions in a well-de\"ined and precise way. This framework can be used to compare and merge models at different abstraction levels; in particular, higher-level (e.g. mobility) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. As examples, we formalize in our framework the vesiculation and the phagocytosis processes

Causal static analysis for Brane Calculi

We present here a static analysis, based on Abstract Interpretation, obtained by defining an abstract version of the causal semantics for the Mate/Bud/Drip (MBD) version of Brane Calculi, proposed by Busi. Our analysis statically approximates the dynamic behaviour of MBD systems. More precisely, the analysis is able to describe the essential behaviour of the represented membranes, in terms of their possible interactions. Furthermore, our analysis is able to statically capture the possible causal dependencies among interactions, whose determination can be exploited to better understand the modelled biological phenomena. Finally, we apply our analysis to an abstract specification of the receptor-mediated endocytosis mechanism

Programming distributed and adaptable autonomous components--the GCM/ProActive framework

International audienceComponent-oriented software has become a useful tool to build larger and more complex systems by describing the application in terms of encapsulated, loosely coupled entities called components. At the same time, asynchronous programming patterns allow for the development of efficient distributed applications. While several component models and frameworks have been proposed, most of them tightly integrate the component model with the middleware they run upon. This intertwining is generally implicit and not discussed, leading to entangled, hard to maintain code. This article describes our efforts in the development of the GCM/ProActive framework for providing distributed and adaptable autonomous components. GCM/ProActive integrates a component model designed for execution on large-scale environments, with a programming model based on active objects allowing a high degree of distribution and concurrency. This new integrated model provides a more powerful development, composition, and execution environment than other distributed component frameworks. We illustrate that GCM/ProActive is particularly adapted to the programming of autonomic component systems, and to the integration into a service-oriented environment