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Bigraphs and Mobile Processes
, 2003
"... A bigraphical reactive system (BRS) involves bigraphs, in which the nesting of nodes represents locality, independently of the edges connecting them; it also allows bigraphs to reconfigure themselves. BRSs aim to provide a uniform way to model spatially distributed systems that both compute and comm ..."
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Cited by 995 (29 self)
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A bigraphical reactive system (BRS) involves bigraphs, in which the nesting of nodes represents locality, independently of the edges connecting them; it also allows bigraphs to reconfigure themselves. BRSs aim to provide a uniform way to model spatially distributed systems that both compute and communicate. In this memorandum we develop their static and dynamic theory. In part I, we illustrate...
A tutorial on EMPA: A theory of concurrent processes with nondeterminism, priorities, probabilities and time
 Theoretical Computer Science
, 1998
"... In this tutorial we give an overview of the process algebra EMPA, a calculus devised in order to model and analyze features of realworld concurrent systems such as nondeterminism, priorities, probabilities and time, with a particular emphasis on performance evaluation. The purpose of this tutorial ..."
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Cited by 95 (9 self)
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In this tutorial we give an overview of the process algebra EMPA, a calculus devised in order to model and analyze features of realworld concurrent systems such as nondeterminism, priorities, probabilities and time, with a particular emphasis on performance evaluation. The purpose of this tutorial is to explain the design choices behind the development of EMPA and how the four features above interact, and to show that a reasonable trade off between the expressive power of the calculus and the complexity of its underlying theory has been achieved.
Bigraphs and Mobile Processes (revised)
, 2004
"... A bigraphical reactive system (BRS) involves bigraphs, in which the nesting of nodes represents locality, independently of the edges connecting them; it also allows bigraphs to reconfigure themselves. BRSs aim to provide a uniform way to model spatially distributed systems that both compute and comm ..."
Abstract

Cited by 59 (6 self)
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A bigraphical reactive system (BRS) involves bigraphs, in which the nesting of nodes represents locality, independently of the edges connecting them; it also allows bigraphs to reconfigure themselves. BRSs aim to provide a uniform way to model spatially distributed systems that both compute and communicate. In this memorandum we develop their static and dynamic theory. In Part I we illustrate...
Probabilistic model checking of complex biological pathways
, 2006
"... Abstract. Probabilistic model checking is a formal verification technique that has been successfully applied to the analysis of systems from a broad range of domains, including security and communication protocols, distributed algorithms and power management. In this paper we illustrate its applicab ..."
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Cited by 59 (11 self)
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Abstract. Probabilistic model checking is a formal verification technique that has been successfully applied to the analysis of systems from a broad range of domains, including security and communication protocols, distributed algorithms and power management. In this paper we illustrate its applicability to a complex biological system: the FGF (Fibroblast Growth Factor) signalling pathway. We give a detailed description of how this case study can be modelled in the probabilistic model checker PRISM, discussing some of the issues that arise in doing so, and show how we can thus examine a rich selection of quantitative properties of this model. We present experimental results for the case study under several different scenarios and provide a detailed analysis, illustrating how this approach can be used to yield a better understanding of the dynamics of the pathway. 1
Pure bigraphs: structure and dynamics
, 2005
"... Bigraphs are graphs whose nodes may be nested, representing locality, independently of the edges connecting them. They may be equipped with reaction rules, forming a bigraphical reactive system (Brs) in which bigraphs can reconfigure themselves. Following an earlier paper describing link graphs, a c ..."
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Cited by 51 (5 self)
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Bigraphs are graphs whose nodes may be nested, representing locality, independently of the edges connecting them. They may be equipped with reaction rules, forming a bigraphical reactive system (Brs) in which bigraphs can reconfigure themselves. Following an earlier paper describing link graphs, a constituent of bigraphs, this paper is a devoted to pure bigraphs, which in turn underlie various more refined forms. Elsewhere it is shown that behavioural analysis for Petri nets, πcalculus and mobile ambients can all be recovered in the uniform framework of bigraphs. The paper first develops the dynamic theory of an abstract structure, a wide reactive system (Wrs), of which a Brs is an instance. In this context, labelled transitions are defined in such a way that the induced bisimilarity is a congruence. This work is then specialised to Brss, whose graphical structure allows many refinements of the theory. The latter part of the paper emphasizes bigraphical theory that is relevant to the treatment of dynamics via labelled transitions. As a running example, the theory is applied to finite pure CCS, whose resulting transition system and bisimilarity are analysed in detail. The paper also mentions briefly the use of bigraphs to model pervasive computing and
PEPA nets: A structured performance modelling formalism
 Performance Evaluation
, 2003
"... In this paper we describe a formalism which uses the stochastic process algebra PEPA as the inscription language for labelled stochastic Petri nets. Viewed in another way, the net is used to provide a structure for linking related PEPA systems. The combined modelling language naturally represents su ..."
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Cited by 34 (22 self)
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In this paper we describe a formalism which uses the stochastic process algebra PEPA as the inscription language for labelled stochastic Petri nets. Viewed in another way, the net is used to provide a structure for linking related PEPA systems. The combined modelling language naturally represents such applications as mobile code systems where the PEPA terms are used to model the program code which moves between network hosts (the places in the net). We describe the implementation of a tool to support this modelling formalism and apply this to model a hierarchical cellular network. 1
Stochastic concurrent constraint programming
 In Proceedings of 4th International Workshop on Quantitative Aspects of Programming Languages, QAPL 2006, ENTCS
, 2006
"... We tackle the problem of relating models of systems (mainly biological systems) based on stochastic process algebras (SPA) with models based on differential equations. We define a syntactic procedure that translates programs written in stochastic Concurrent Constraint Programming (sCCP) into a set o ..."
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Cited by 33 (12 self)
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We tackle the problem of relating models of systems (mainly biological systems) based on stochastic process algebras (SPA) with models based on differential equations. We define a syntactic procedure that translates programs written in stochastic Concurrent Constraint Programming (sCCP) into a set of Ordinary Differential Equations (ODE), and also the inverse procedure translating ODE’s into sCCP programs. For the class of biochemical reactions, we show that the translation is correct w.r.t. the intended rate semantics of the models. Finally, we show that the translation does not generally preserve the dynamical behavior, giving a list of open research problems in this direction.
A Graphical Representation for Biological Processes in the Stochastic picalculus
 Transactions in Computational Systems Biology
, 2006
"... Abstract. This paper presents a graphical representation for the stochastic πcalculus, which is formalised by defining a corresponding graphical calculus. The graphical calculus is shown to be reduction equivalent to stochastic π, ensuring that the two calculi have the same expressive power. The gr ..."
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Cited by 32 (14 self)
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Abstract. This paper presents a graphical representation for the stochastic πcalculus, which is formalised by defining a corresponding graphical calculus. The graphical calculus is shown to be reduction equivalent to stochastic π, ensuring that the two calculi have the same expressive power. The graphical representation is used to model a couple of example biological systems, namely a bistable gene network and a mapk signalling cascade. One of the benefits of the representation is its ability to highlight the existence of cycles, which are a key feature of biological systems. Another benefit is its ability to animate interactions between system components, in order to visualise system dynamics. The graphical representation can also be used as a front end to a simulator for the stochastic πcalculus, to help make modelling and simulation of biological systems more accessible to non computer scientists. 1
A fluid analysis framework for a Markovian process algebra
, 2010
"... Markovian process algebras, such as PEPA and stochastic πcalculus, bring a powerful compositional approach to the performance modelling of complex systems. However, the models generated by process algebras, as with other interleaving formalisms, are susceptible to the state space explosion problem. ..."
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Cited by 28 (23 self)
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Markovian process algebras, such as PEPA and stochastic πcalculus, bring a powerful compositional approach to the performance modelling of complex systems. However, the models generated by process algebras, as with other interleaving formalisms, are susceptible to the state space explosion problem. Models with only a modest number of process algebra terms can easily generate so many states that they are all but intractable to traditional solution techniques. Previous work aimed at addressing this problem has presented a fluidflow approximation allowing the analysis of systems which would otherwise be inaccessible. To achieve this, systems of ordinary differential equations describing the fluid flow of the stochastic process algebra model are generated informally. In this paper, we show formally that for a large class of models, this fluidflow analysis can be directly derived from the stochastic process algebra model as an approximation to the mean number of component types within the model. The nature of the fluid approximation is derived and characterised by direct comparison with the Chapman–Kolmogorov equations underlying the Markov model. Furthermore, we compare the fluid approximation with the exact solution using stochastic simulation and we are able to demonstrate that it is a very accurate approximation in many cases. For the first time, we also show how to extend these techniques naturally to generate systems of differential equations approximating higher order moments of model component counts. These are important performance characteristics for estimating, for instance, the variance of the component counts. This is very necessary if we are to understand how precise the fluidflow calculation is, in a given modelling situation.
Transition systems, link graphs and Petri nets
, 2004
"... A framework is defined within which reactive systems can be studied formally. The framework is based upon scategories, a new variety of categories, within which reactive systems can be set up in such a way that labelled transition systems can be uniformly extracted. These lead in turn to behavi ..."
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Cited by 26 (5 self)
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A framework is defined within which reactive systems can be studied formally. The framework is based upon scategories, a new variety of categories, within which reactive systems can be set up in such a way that labelled transition systems can be uniformly extracted. These lead in turn to behavioural preorders and equivalences, such as the failures preorder (treated elsewhere) and bisimilarity, which are guaranteed to be congruential. The theory rests upon the notion of relative pushout previously introduced by the authors. The framework