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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 62 (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
Bigraphical Models of Contextaware Systems
, 2005
"... As part of ongoing work on evaluating Milner’s bigraphical reactive systems, we investigate bigraphical models of contextaware systems, a facet of ubiquitous computing. We find that naively encoding such systems in bigraphs is somewhat awkward; and we propose a more sophisticated modeling technique ..."
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Cited by 36 (15 self)
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As part of ongoing work on evaluating Milner’s bigraphical reactive systems, we investigate bigraphical models of contextaware systems, a facet of ubiquitous computing. We find that naively encoding such systems in bigraphs is somewhat awkward; and we propose a more sophisticated modeling technique, introducing Platographical models, alleviating this awkwardness. We argue that such models are useful for simulation and point out that for reasoning about such bigraphical models, the bisimilarity inherent to bigraphical reactive systems is not enough in itself; an equivalence between the bigraphical reactive systems themselves is also needed.
Spatial Logics for Bigraphs
 In Proceedings of ICALP’05, volume 3580 of LNCS
, 2005
"... Abstract. Bigraphs are emerging as an interesting model for concurrent calculi, like CCS, picalculus, and Petri nets. Bigraphs are built orthogonally on two structures: a hierarchical place graph for locations and a link (hyper)graph for connections. With the aim of describing bigraphical structur ..."
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Cited by 27 (3 self)
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Abstract. Bigraphs are emerging as an interesting model for concurrent calculi, like CCS, picalculus, and Petri nets. Bigraphs are built orthogonally on two structures: a hierarchical place graph for locations and a link (hyper)graph for connections. With the aim of describing bigraphical structures, we introduce a general framework for logics whose terms represent arrows in monoidal categories. We then instantiate the framework to bigraphical structures and obtain a logic that is a natural composition of a place graph logic and a link graph logic. We explore the concepts of separation and sharing in these logics and we prove that they generalise some known spatial logics for trees, graphs and tree contexts. 1
Matching of Bigraphs
 PREPRINT OF GTVC 2006
, 2006
"... We analyze the matching problem for bigraphs. In particular, we present a sound and complete inductive characterization of matching of binding bigraphs. Our results pave the way for a provably correct matching algorithm, as needed for an implementation of bigraphical reactive systems. ..."
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Cited by 24 (12 self)
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We analyze the matching problem for bigraphs. In particular, we present a sound and complete inductive characterization of matching of binding bigraphs. Our results pave the way for a provably correct matching algorithm, as needed for an implementation of bigraphical reactive systems.
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways
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The Calculus of Looping Sequences
"... Abstract. We describe the Calculus of Looping Sequences (CLS) which is suitable for modeling microbiological systems and their evolution. We present two extensions, CLS with links (LCLS) and Stochastic CLS. LCLS simplifies the description of protein interaction at a lower level of abstraction, namel ..."
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Cited by 16 (4 self)
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Abstract. We describe the Calculus of Looping Sequences (CLS) which is suitable for modeling microbiological systems and their evolution. We present two extensions, CLS with links (LCLS) and Stochastic CLS. LCLS simplifies the description of protein interaction at a lower level of abstraction, namely at the domain level. Stochastic CLS allows us to describe quantitative aspects of the modeled systems, such as the frequency of chemical reactions. As examples of application to real biological systems, we show the simulation of the activity of the lactose operon in E.coli and the quorum sensing process in P.aeruginosa, both described with Stochastic CLS. 1
A Type System for a Stochastic CLS
, 2009
"... The Stochastic Calculus of Looping Sequences is suitable to describe the evolution of microbiological systems, taking into account the speed of the described activities. We propose a type system for this calculus that models how the presence of catalysers and inhibitors can modify these speeds. We c ..."
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Cited by 10 (9 self)
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The Stochastic Calculus of Looping Sequences is suitable to describe the evolution of microbiological systems, taking into account the speed of the described activities. We propose a type system for this calculus that models how the presence of catalysers and inhibitors can modify these speeds. We claim that types are the right abstraction in order to represent the interaction between elements without specifying exactly the element positions. Our claim is supported through an example modelling the lactose operon.
A.: On designing multicoreaware simulators for biological systems
 In: Proc. of Intl. Euromicro PDP 2011: Parallel Distributed and networkbased Processing
"... Abstract—The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to speed it up on multicore platforms, which pose new ..."
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Cited by 9 (5 self)
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Abstract—The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to speed it up on multicore platforms, which pose new challenges for parallelisation techniques. These opportunities are developed in two general families of solutions involving both the single simulation and a bulk of independent simulations (either replicas of derived from parameter sweep). Proposed solutions are tested on the parallelisation of the CWC simulator (Calculus of Wrapped Compartments) that is carried out according to proposed solutions by way of the FastFlow programming framework making possible fast development and efficient execution on multicores. Index Terms—multicore; parallel simulation; stochastic simulation; SIMD; lockfree synchronisation; I.
Multilevel modelling via stochastic multilevel multiset rewriting
 MATHEMATICAL STRUCTURES IN COMPUTER SCIENCE
, 2011
"... We present a simple stochastic rulebased approach to multilevel modelling for computational systems biology. Populations are modelled using multilevel multisets; these contain both species and agents, with the latter possibly containing further such multisets. Rules are pairs of such multisets, bu ..."
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Cited by 9 (1 self)
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We present a simple stochastic rulebased approach to multilevel modelling for computational systems biology. Populations are modelled using multilevel multisets; these contain both species and agents, with the latter possibly containing further such multisets. Rules are pairs of such multisets, but now allowing variables to occur (as well as species and agents), together with an associated stochastic rate. We give two illustrative examples. The first is an extracellular model of virus infection, coupled with an intracellular model of viral reproduction; this model can demonstrate successive waves of infection. The second is a model of cell division in which a repressor protein is diluted in successive generations, when repression no longer occurs. The multilevel multiset approach can also be seen in terms of stochastic term rewriting for the theory of a commutative monoid, equipped with extra constants (for the species) and unary operations (for the agents). We further discuss the relationship of this approach with two others: Krivine et al.’s stochastic bigraphs, restricted to Milner’s place graphs, and Coppo et al.’s Stochastic Calculus of Wrapped Compartments. These various relationships provide evidence for the fundamental nature of the approach.
Multistep Attack Modelling and Simulation (MsAMS) Framework based on Mobile Ambients
, 2008
"... Attackers take advantage of any security breach to penetrate an organisation perimeter and exploit hosts as stepping stones to reach valuable assets, deeper in the network. The exploitation of hosts is possible not only when vulnerabilities in commercial offtheshelf (COTS) software components are ..."
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Cited by 8 (1 self)
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Attackers take advantage of any security breach to penetrate an organisation perimeter and exploit hosts as stepping stones to reach valuable assets, deeper in the network. The exploitation of hosts is possible not only when vulnerabilities in commercial offtheshelf (COTS) software components are present, but also, for example, when an attacker acquires a credential on one host which allows exploiting further hosts on the network. Finding attacks involving the latter case requires the ability to represent dynamic models. In fact, more dynamic aspects are present in the network domain such as attackers accumulate resources (i.e. credentials) along an attack, and users and assets may move from one environment to another, although always constrained by the ruling of the network. In this paper we address these dynamic issues by presenting MsAMS (Multistep Attack Modelling and Simulation), an implemented framework, based on Mobile Ambients, to discover attacks in networks. The idea of ambients fits naturally into this domain and has the advantage of providing flexibility for modelling. Additionally, the concept of mobility allows the simulation of attackers exploiting opportunities derived either from the exploitation of vulnerable and nonvulnerable hosts, through the acquisition of credentials. It also allows expressing security policies embedded in the rules of the ambients.