Type Inference for the receptive distributed Pi-calculus

In this paper we study the type inference problem for an extended version of the type system of d_1^r very closed to the one of Hennessy and Riely's d. These are distributed Pi-calculus involving explicit notions of locations and migration where the location space is flat and communication is local. Moreover, location names are typed and we use an explicit subtyping relation over location types that enable us to define a notion of principal typing. We provide an inference type algorithm computing a principal type for all typable term

Theoretical basis of the community effect in development

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A Stochastic Pi Calculus for Concurrent Objects

International audienceWe present SpiCO, a new modeling and simulation language for system biology, based on the stochastic pi-calculus. SpiCO supports higher level modeling via multi-profile concurrent objects with static inheritance. We present a semantics for SpiCO in terms of continuous time Markov chains, and show how to compile SpiCO back into the biochemical stochastic pi-calculus while preserving semantics

Dynamic Compartments in the Imperative Pi Calculus

International audienceDynamic compartments with mutable configurations and variable volumes are of basic interest for the stochastic modeling of biochemistry in cells. We propose a new language to express dynamic compartments that we call the imperative π-calculus. It is obtained from the attributed π-calculus by adding imperative assignment operations to a global store. Previous approaches to dynamic compartments are improved in flexibility or efficiency. This is illustrated by an appropriate model of osmosis and a correct encoding of BioAmbients

The Receptive Distributed π\pi-Calculus

In this paper we study an asynchronous distributed $\pi$-calculus, with constructs for localities and migration. We show that a simple static analysis ensures the receptiveness of channel names, which, together with a simple type system, guarantees a local deadlock-freedom property, that we call message deliverability. This property states that any migrating message will find an appropriate receiver at its destination locality. We argue that this distributed, receptive calculus is still expressive enough, by giving a series of examples illustrating the «receptive style» of programming we have. Finally we show that our calculus contains the $\pi_1$-calculus, up to weak asynchronous bisimulation

Structural simplification of chemical reaction networks preserving deterministic semantics

International audienceWe study the structural simplification of chemical reaction networks preserving the deterministic kinetics. We aim at finding simplification rules that can eliminate intermediate molecules while preserving the dynamics of all others. The rules should be valid even though the network is plugged into a bigger context. An example is Michaelis-Menten's simplification rule for enzymatic reactions. In this paper, we present a large class of structural simplification rules for reaction networks that can eliminate intermediate molecules at equilibrium, without assuming that all molecules are at equilibrium, i.e. in a steady state. We prove the correctness of our simplification rules for all contexts that preserve the equilibrium of the eliminated molecules. Finally, we illustrate at a concrete example network from systems biology that our simplification rules may allow to drastically reduce the size of reaction networks in practice

Attractor Equivalence: An Observational Semantics for Reaction Networks

International audienceWe study observational semantics for networks of chemical reactions as used in systems biology. Reaction networks without kinetic information, as we consider, can be identified with Petri nets. We present a new observational semantics for reaction networks that we call the attractor equivalence. The main idea of the attractor equivalence is to observe reachable attractors and reachability of an attractor divergence in all possible contexts. The attractor equivalence can support powerful simplifications for reaction networks as we illustrate at the example of the Tet-On system. Alternative semantics based on bisimulations or traces, in contrast, do not support all needed simplifications

A Stochastic Pi Calculus for Concurrent Objects

International audienceWe present SpiCO, a new modeling and simulation language for system biology, based on the stochastic pi-calculus. SpiCO supports higher level modeling via multi-profile concurrent objects with static inheritance. We present a semantics for SpiCO in terms of continuous time Markov chains, and show how to compile SpiCO back into the biochemical stochastic pi-calculus while preserving semantics

Models of Tet-On System with Epigenetic Effects

International audienceWe present the first results of ongoing work investigating two models of the artificial inducible promoter Tet-On that include epigenetic regulation. We consider chromatin states and 1D diffusion of transcription factors that reveal, respectively, stochastic noise and a memory effect

The Attributed Pi Calculus

International audienceThe attributed pi calculus (pi(L)) forms an extension of the pi calculus with attributed processes and attribute dependent synchronization. To ensure flexibility, the calculus is parametrized with the language L which defines possible values of attributes. pi(L) can express polyadic synchronization as in pi@ and thus diverse compartment organizations. A non-deterministic and a stochastic semantics, where rates may depend on attribute values, is introduced. The stochastic semantics is based on continuous time Markov chains. A simulation algorithm is developed which is firmly rooted in this stochastic semantics. Two examples, the movement processes in the phototaxis of Euglena and the cooperative binding in the gene regulation of the lambda Phage, underline the applicability of pi(L) to systems biology