Dynamic Compartments in the Imperative π-Calculus

John, Mathias; Lhoussaine, Cédric; Niehren, Joachim

doi:10.1007/978-3-642-03845-7_16

Cited by 15 publications

(10 citation statements)

References 22 publications

(34 reference statements)

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“…First, it must be investigated to what extent the introduction of functional rates in bio-oriented process calculi semantics can be pushed, in particular in those calculi equipped with high-level structural rearrangement primitives (for example, calculi with nested compartments [6,33]). Moreover, it is still unclear how this approach can be adapted to cope with more sophisticated calculi like [26,25], where functional rates have been already introduced but with a different technique, based on communication constraints. A special case is the React(C) language [27], that can be regarded as an extension of Kappa as well as of κ F , but differently from κ F the functional rate takes under consideration the entire system (i.e.…”

Section: Resultsmentioning

confidence: 99%

Complex Functional Rates in Rule-Based Languages for Biochemistry

Versari

Zavattaro

2012

Lecture Notes in Computer Science

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Rule-based languages (like, for example, Kappa, BioNetGen, and BioCham) have emerged as successful models for the representation, analysis, and simulation of bio-chemical systems. In particular Kappa, although based on reactions, differs from traditional chemistry as it allows for a graph-like representation of complexes. It follows the "don't care, don't write" approach: a rule contains the description of only those parts of the complexes that are actually involved in a reaction. Hence, given any possible combination of complexes that contain the reactants, such complexes can give rise to the reaction. In this paper we address the problem of extending the "don't care, don't write" approach to cases in which the actual structure of the complexes involved in the reaction could affect it (for instance, the mass of the complexes could influence the rate). The solutions that we propose is κF , an extension of the Kappa-calculus in which rates are defined as functions of the actually involved complexes.

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Section: Resultsmentioning

confidence: 99%

Complex Functional Rates in Rule-Based Languages for Biochemistry

Versari

Zavattaro

2012

Lecture Notes in Computer Science

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“…The imperative π-calculus [14] is a recent extension of the attribute π-calculus with a global store and with imperative programs used to specify constraints.…”

Section: Discussion and Related Workmentioning

confidence: 99%

On the Power of Attribute-Based Communication

Alrahman

Nicola

Loreti

2016

Formal Techniques for Distributed Objects, Components, and Systems

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Abstract. In open systems, i.e. systems operating in an environment that they cannot control and with components that may join or leave, behaviors can arise as side effects of intensive components interaction. Finding ways to understand and design these systems and, most of all, to model the interactions of their components, is a difficult but important endeavor. To tackle these issues, we present AbC , a calculus for attributebased communication. An AbC system consists of a set of parallel agents each of which is equipped with a set of attributes. Communication takes place in an implicit multicast fashion, and interactions among agents are dynamically established by taking into account "connections" as determined by predicates over the attributes of agents. First, the syntax and the semantics of the calculus are presented, then expressiveness and effectiveness of AbC are demonstrated both in terms of modeling scenarios featuring collaboration, reconfiguration, and adaptation and of the possibility of encoding channel-based interactions and other interaction patterns. Behavioral equivalences for AbC are introduced for establishing formal relationships between different descriptions of the same system.

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“…The imperative π-calculus is a recent extension of the attributed π-calculus with a global imperative store [44]. The original motivation was to enable a simpler encoding of dynamic compartments, that does not rely on priorities.…”

Section: Discussionmentioning

confidence: 99%

“…This example indicates, that priorities might permit to implement individualbased models with global stores, as proposed in [44].…”

Section: Global Information In Individual-based Modelingmentioning

confidence: 96%