We introduce a labelled transition semantics for the reversible π-calculus. It is the first account of a compositional definition of a reversible calculus, that has both concurrency primitives and name mobility.The notion of reversibility is strictly linked to the notion of causality. We discuss the notion of causality induced by our calculus, and we compare it with the existing notions in the literature, in particular for what concerns the syntactic feature of scope extrusion, typical of the π-calculus.

MotivationWe present an overview of the Kappa platform, an integrated suite of analysis and visualization techniques for building and interactively exploring rule-based models. The main components of the platform are the Kappa Simulator, the Kappa Static Analyzer and the Kappa Story Extractor. In addition to these components, we describe the Kappa User Interface, which includes a range of interactive visualization tools for rule-based models needed to make sense of the complexity of biological systems. We argue that, in this approach, modeling is akin to programming and can likewise benefit from an integrated development environment. Our platform is a step in this direction.ResultsWe discuss details about the computation and rendering of static, dynamic, and causal views of a model, which include the contact map (CM), snaphots at different resolutions, the dynamic influence network (DIN) and causal compression. We provide use cases illustrating how these concepts generate insight. Specifically, we show how the CM and snapshots provide information about systems capable of polymerization, such as Wnt signaling. A well-understood model of the KaiABC oscillator, translated into Kappa from the literature, is deployed to demonstrate the DIN and its use in understanding systems dynamics. Finally, we discuss how pathways might be discovered or recovered from a rule-based model by means of causal compression, as exemplified for early events in EGF signaling.Availability and implementationThe Kappa platform is available via the project website at kappalanguage.org. All components of the platform are open source and freely available through the authors’ code repositories.

Contextual equivalence equate terms that have the same observable behaviour in any context. A standard contextual equivalence for CCS is the strong barbed congruence. Configuration structures are a denotational semantics for processes in which one define equivalences that are more discriminating, i.e. that distinguish the denotation of terms equated by barbed congruence. Hereditary history preserving bisimulation (HHPB) is such a relation. We define a strong backand-forth barbed congruence on RCCS, a reversible variant of CCS. We show that the relation induced by the back-and-forth congruence on configuration structures is equivalent to HHPB, thus providing a contextual characterization of HHPB.

No abstract

No abstract

A standard contextual equivalence for process algebras is strong barbed congruence. Configuration structures are a denotational semantics for processes in which one can define equivalences that are more discriminating, i.e. that distinguish the denotation of terms equated by barbed congruence. Hereditary history preserving bisimulation (HHPB) is such a relation. We define a strong back and forth barbed congruence using a reversible process algebra and show that the relation induced by the back and forth congruence is equivalent to HHPB, providing a contextual characterization of HHPB.

HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Copyright

Graph rewrite formalisms are a powerful approach to modeling complex molecular systems. They capture the intrinsic concurrency of molecular interactions, thereby enabling a formal notion of mechanism (a partially ordered set of events) that explains how a system achieves a particular outcome given a set of rewrite rules. It is then useful to verify whether the mechanisms that emerge from a given model comply with empirical observations about their mutual interference. In this work, our objective is to determine whether a specific event in the mechanism for achieving X prevents or promotes the occurrence of a specific event in the mechanism for achieving Y. Such checks might also be used to hypothesize rules that would bring model mechanisms in compliance with observations. We define a rigorous framework for defining the concept of interference (positive or negative) between mechanisms induced by a system of graph-rewrite rules and for establishing whether an asserted influence can be realized given two mechanisms as an input.