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56
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 1000 (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...
Rulebased Modelling of Cellular Signalling
 Proceedings of the 18 th International Conference on Concurrency Theory (CONCUR’07), Lecture Notes in Computer Science
, 2007
"... Abstract. Modelling is becoming a necessity in studying biological signalling pathways, because the combinatorial complexity of such systems rapidly overwhelms intuitive and qualitative forms of reasoning. Yet, this same combinatorial explosion makes the traditional modelling paradigm based on syste ..."
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Cited by 70 (18 self)
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Abstract. Modelling is becoming a necessity in studying biological signalling pathways, because the combinatorial complexity of such systems rapidly overwhelms intuitive and qualitative forms of reasoning. Yet, this same combinatorial explosion makes the traditional modelling paradigm based on systems of differential equations impractical. In contrast, agentbased or concurrent languages, such as κ [1–3] or the closely related BioNetGen language [4–10], describe biological interactions in terms of rules, thereby avoiding the combinatorial explosion besetting differential equations. Rules are expressed in an intuitive graphical form that transparently represents biological knowledge. In this way, rules become a natural unit of model building, modification, and discussion. We illustrate this with a sizeable example obtained from refactoring two models of EGF receptor signalling that are based on differential equations [11, 12]. An exciting aspect of the agentbased approach is that it naturally lends itself to the identification and analysis of the causal structures that deeply shape the dynamical, and perhaps even evolutionary, characteristics of complex distributed biological systems. In particular, one can adapt the notions of causality and conflict, familiar from concurrency theory, to κ, our representation language of choice. Using the EGF receptor model as an example, we show how causality enables the formalization of the colloquial concept of pathway and, perhaps more surprisingly, how conflict can be used to dissect the signalling dynamics to obtain a qualitative handle on the range of system behaviours. By taming the combinatorial explosion, and exposing the causal structures and key kinetic junctures in a model, agent and rulebased representations hold promise for making modelling more powerful, more perspicuous, and of appeal to a wider audience. 1
Deriving Bisimulation Congruences in the DPO Approach to Graph Rewriting
, 2004
"... Motivated by recent work on the derivation of labelled transitions and bisimulation congruences from unlabelled reaction rules, we show how to solve this problem in the DPO (doublepushout) approach to graph rewriting. Unlike in previous approaches, we consider graphs as objects, instead of arrows, ..."
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Cited by 61 (10 self)
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Motivated by recent work on the derivation of labelled transitions and bisimulation congruences from unlabelled reaction rules, we show how to solve this problem in the DPO (doublepushout) approach to graph rewriting. Unlike in previous approaches, we consider graphs as objects, instead of arrows, of the category under consideration. This allows us to present a very simple way of deriving labelled transitions (called rewriting steps with borrowed context) which smoothly integrates with the DPO approach, has a very constructive nature and requires only a minimum of category theory. The core part of this paper is the proof sketch that the bisimilarity based on rewriting with borrowed contexts is a congruence relation.
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 ..."
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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...
A brief history of process algebra
 Theor. Comput. Sci
, 2004
"... Abstract. This note addresses the history of process algebra as an area of research in concurrency theory, the theory of parallel and distributed systems in computer science. Origins are traced back to the early seventies of the twentieth century, and developments since that time are sketched. The a ..."
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Cited by 56 (1 self)
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Abstract. This note addresses the history of process algebra as an area of research in concurrency theory, the theory of parallel and distributed systems in computer science. Origins are traced back to the early seventies of the twentieth century, and developments since that time are sketched. The author gives his personal views on these matters. He also considers the present situation, and states some challenges for the future.
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 50 (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
Axioms For Bigraphical Structure
 UNDER CONSIDERATION FOR PUBLICATION IN MATH. STRUCT. IN COMP. SCIENCE
, 2005
"... This paper axiomatises the structure of bigraphs, and proves that the resulting theory is complete. Bigraphs are graphs with double structure, representing locality and connectivity. They have been shown to represent dynamic theories for the #calculus, mobile ambients and Petri nets, in a way th ..."
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Cited by 36 (8 self)
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This paper axiomatises the structure of bigraphs, and proves that the resulting theory is complete. Bigraphs are graphs with double structure, representing locality and connectivity. They have been shown to represent dynamic theories for the #calculus, mobile ambients and Petri nets, in a way that is faithful to each of those models of discrete behaviour. While the main purpose of bigraphs is to understand mobile systems, a prerequisite for this understanding is a wellbehaved theory of the structure of states in such systems. The algebra of bigraph structure is surprisingly simple, as the paper demonstrates; this is because bigraphs treat locality and connectivity orthogonally
Reactive Systems over Cospans
, 2005
"... The theory of reactive systems, introduced by Leifer and Milner and previously extended by the authors, allows the derivation of wellbehaved labelled transition systems (LTS) for semantic models with an underlying reduction semantics. The derivation procedure requires the presence of certain colimi ..."
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Cited by 36 (2 self)
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The theory of reactive systems, introduced by Leifer and Milner and previously extended by the authors, allows the derivation of wellbehaved labelled transition systems (LTS) for semantic models with an underlying reduction semantics. The derivation procedure requires the presence of certain colimits (or, more usually and generally, bicolimits) which need to be constructed separately within each model. In this paper, we o#er a general construction of such bicolimits in a class of bicategories of cospans. The construction sheds light on as well as extends Ehrig and Konig's rewriting via borrowed contexts and opens the way to a unified treatment of several applications.
Saturated semantics for reactive systems
 LOGIC IN COMPUTER SCIENCE
, 2006
"... The semantics of process calculi has traditionally been specified by labelled transition systems (LTS), but with the development of name calculi it turned out that reaction rules (i.e., unlabelled transition rules) are often more natural. This leads to the question of how behavioural equivalences (b ..."
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Cited by 27 (15 self)
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The semantics of process calculi has traditionally been specified by labelled transition systems (LTS), but with the development of name calculi it turned out that reaction rules (i.e., unlabelled transition rules) are often more natural. This leads to the question of how behavioural equivalences (bisimilarity, trace equivalence, etc.) defined for LTS can be transferred to unlabelled transition systems. Recently, in order to answer this question, several proposals have been made with the aim of automatically deriving an LTS from reaction rules in such a way that the resulting equivalences are congruences. Furthermore these equivalences should agree with the intended semantics, whenever one exists. In this paper we propose saturated semantics, based on a weaker notion of observation and orthogonal to all the previous proposals, and we demonstrate the appropriateness of our semantics by means of two examples: logic programming and a subset of the open πcalculus. Indeed, we prove that our equivalences are congruences and that they coincide with logical equivalence and open bisimilarity respectively, while equivalences studied in previous works are strictly finer.
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