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13
Scalable simulation of cellular signaling networks
 In Proceedings of APLAS 2007
, 2007
"... Abstract. Given the combinatorial nature of cellular signalling pathways, where biological agents can bind and modify each other in a large number of ways, concurrent or agentbased languages seem particularly suitable for their representation and simulation [1–4]. Graphical modelling languages such ..."
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Cited by 33 (11 self)
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Abstract. Given the combinatorial nature of cellular signalling pathways, where biological agents can bind and modify each other in a large number of ways, concurrent or agentbased languages seem particularly suitable for their representation and simulation [1–4]. Graphical modelling languages such as κ [5–8], or the closely related BNG language [9– 14], seem to afford particular ease of expression. It is unclear however how such models can be implemented. 6 Even a simple model of the EGF receptor signalling network can generate more than 10 23 nonisomorphic species [5], and therefore no approach to simulation based on enumerating species (beforehand, or even onthefly) can handle such models without sampling down the number of potential generated species. We present in this paper a radically different method which does not attempt to count species. The proposed algorothm uses a representation of the system together with a superapproximation of its ‘event horizon ’ (all events that may happen next), and a specific correction scheme to obtain exact timings. Being completely local and not based on any kind of enumeration, this algorithm has a per event time cost which is independent of (i) the size of the set of generable species (which can even be infinite), and (ii) independent of the size of the system (ie, the number of agent instances). We show how to refine this algorithm, using concepts derived from the classical notion of causality, so that in addition to the above one also has that the even cost is depending (iii) only logarithmically on the size of the model (ie, the number of rules). Such complexity properties reflect in our implementation which, on a current computer, generates about 10 6 events per minute in the case of the simple EGF receptor model mentioned above, using a system with 10 5 agents. 1
Reversible communicating systems
 in: CONCUR’04, LNCS 3170 (2004
, 2004
"... Abstract. One obtains in this paper a process algebra RCCS, in the style of CCS, where processes can backtrack. Backtrack, just as plain forward computation, is seen as a synchronization and incurs no additional cost on the communication structure. It is shown that, given a past, a computation step ..."
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Cited by 28 (4 self)
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Abstract. One obtains in this paper a process algebra RCCS, in the style of CCS, where processes can backtrack. Backtrack, just as plain forward computation, is seen as a synchronization and incurs no additional cost on the communication structure. It is shown that, given a past, a computation step can be taken back if and only if it leads to a causally equivalent past. 1
Models for NamePassing Processes: Interleaving and Causal
 In Proceedings of LICS 2000: the 15th IEEE Symposium on Logic in Computer Science (Santa Barbara
, 2000
"... We study syntaxfree models for namepassing processes. For interleaving semantics, we identify the indexing structure required of an early labelled transition system to support the usual picalculus operations, defining Indexed Labelled Transition Systems. For noninterleaving causal semantics we de ..."
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Cited by 24 (3 self)
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We study syntaxfree models for namepassing processes. For interleaving semantics, we identify the indexing structure required of an early labelled transition system to support the usual picalculus operations, defining Indexed Labelled Transition Systems. For noninterleaving causal semantics we define Indexed Labelled Asynchronous Transition Systems, smoothly generalizing both our interleaving model and the standard Asynchronous Transition Systems model for CCSlike calculi. In each case we relate a denotational semantics to an operational view, for bisimulation and causal bisimulation respectively. We establish completeness properties of, and adjunctions between, categories of the two models. Alternative indexing structures and possible applications are also discussed. These are first steps towards a uniform understanding of the semantics and operations of namepassing calculi.
Causality in Membrane Systems
"... Summary. P systems are a biologically inspired model introduced by Gheorghe Păun with the aim of representing the structure and the functioning of the cell. P systems are usually equipped with the maximal parallelism semantics; however, since their introduction, some alternative semantics have been ..."
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Cited by 6 (0 self)
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Summary. P systems are a biologically inspired model introduced by Gheorghe Păun with the aim of representing the structure and the functioning of the cell. P systems are usually equipped with the maximal parallelism semantics; however, since their introduction, some alternative semantics have been proposed and investigated. We propose a semantics that describes the causal dependencies occurring between the reactions of a P system. We investigate the basic properties that are satisfied by such a semantics. The notion of causality turns out to be quite relevant for biological systems, as it permits to point out which events occurring in a biological pathway are necessary for another event to happen. 1
Typed event Structures and the πcalculus
 In Proc. MFPS’06
, 2006
"... Abstract. We propose a typing system for the true concurrent model of event structures that guarantees an interesting behavioural property known as confusion freeness. A system is confusion free if nondeterministic choices are localised and do not depend on the scheduling of independent components. ..."
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Cited by 5 (3 self)
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Abstract. We propose a typing system for the true concurrent model of event structures that guarantees an interesting behavioural property known as confusion freeness. A system is confusion free if nondeterministic choices are localised and do not depend on the scheduling of independent components. It is a generalisation of confluence to systems that allow nondeterminism. Ours is the first typing system to control behaviour in a true concurrent model. To demonstrate its applicability, we show that typed event structures give a semantics of linearly typed version of the πcalculi with internal mobility. The semantics we provide is the first event structure semantics of the πcalculus and generalises Winskel’s original event structure semantics of CCS. 1
Compositional Event Structure Semantics for the Internal πCalculus ⋆
"... Abstract. We propose the first compositional event structure semantics for a very expressive πcalculus, generalising Winskel’s event structures for CCS. The πcalculus we model is the πIcalculus with recursive definitions and summations. First we model the synchronous calculus, introducing a notio ..."
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Cited by 3 (0 self)
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Abstract. We propose the first compositional event structure semantics for a very expressive πcalculus, generalising Winskel’s event structures for CCS. The πcalculus we model is the πIcalculus with recursive definitions and summations. First we model the synchronous calculus, introducing a notion of dynamic renaming to the standard operators on event structures. Then we model the asynchronous calculus, for which a new additional operator, called rooting, is necessary for representing causality due to new name binding. The semantics are shown to be operationally adequate and sound with respect to bisimulation. 1
Compositional Event Structure Semantics for the πCalculus
"... Abstract. We propose the first compositional event structure semantics for a fully expressive πcalculus, generalising Winskel’s event structures for CCS. The πcalculus we model is the πIcalculus with recursive definitions and summations. First we model the synchronous calculus, introducing a noti ..."
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Cited by 3 (0 self)
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Abstract. We propose the first compositional event structure semantics for a fully expressive πcalculus, generalising Winskel’s event structures for CCS. The πcalculus we model is the πIcalculus with recursive definitions and summations. First we model the synchronous calculus, introducing a notion of dynamic renaming to the standard operators on event structures. Then we model the asynchronous calculus, for which a new additional operator, called rooting, is necessary for representing causality due to new name binding. The semantics are shown to be operationally adequate and sound with respect to bisimulation. 1
Quantitative testing semantics for noninterleaving
, 2009
"... Abstract. This paper presents a noninterleaving denotational semantics for the πcalculus. The basic idea is to define a notion of test where the outcome is not only whether a given process passes a given test, but also in how many different ways it can pass it. More abstractly, the set of possible ..."
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Cited by 2 (2 self)
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Abstract. This paper presents a noninterleaving denotational semantics for the πcalculus. The basic idea is to define a notion of test where the outcome is not only whether a given process passes a given test, but also in how many different ways it can pass it. More abstractly, the set of possible outcomes for tests forms a semiring, and the set of process interpretations appears as a module over this semiring, in which basic syntactic constructs are affine operators. This notion of test leads to a trace semantics in which traces are partial orders, in the style of Mazurkiewicz traces, extended with readiness information. Our construction has standard may and musttesting as special cases.
Abstract A Chart Semantics for the PiCalculus
"... We present a graphical semantics for the picalculus, that is easier to visualize and better suited to expressing causality and temporal properties than conventional relational semantics. A pichart is a finite directed acyclic graph recording a computation in the picalculus. Each node represents a ..."
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Cited by 1 (0 self)
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We present a graphical semantics for the picalculus, that is easier to visualize and better suited to expressing causality and temporal properties than conventional relational semantics. A pichart is a finite directed acyclic graph recording a computation in the picalculus. Each node represents a process, and each edge either represents a computation step, or a messagepassing interaction. Picharts enjoy a natural pictorial representation, akin to message sequence charts, in which vertical edges represent control flow and horizontal edges represent data flow based on message passing. A pichart represents a single computation starting from its top (the nodes with no ancestors) to its bottom (the nodes with no descendants). Unlike conventional reductions or transitions, the edges in a pichart induce ancestry and other causal relations on processes. We give both compositional and operational definitions of picharts, and illustrate the additional expressivity afforded by the chart semantics via a series of examples.
Quantitative testing semantics for noninterleaving
, 2009
"... Abstract. This paper presents a noninterleaving denotational semantics for the πcalculus. The basic idea is to define a notion of test where the outcome is not only whether a given process passes a given test, but also in how many different ways it can pass it. More abstractly, the set of possible ..."
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Abstract. This paper presents a noninterleaving denotational semantics for the πcalculus. The basic idea is to define a notion of test where the outcome is not only whether a given process passes a given test, but also in how many different ways it can pass it. More abstractly, the set of possible outcomes for tests forms a semiring, and the set of process interpretations appears as a module over this semiring, in which basic syntactic constructs are affine operators. This notion of test leads to a trace semantics in which traces are partial orders, in the style of Mazurkiewicz traces, extended with readiness information. Our construction has standard may and musttesting as special cases. 1