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14
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
Automata with group actions
 In LICS
, 2011
"... Abstract—Our motivating question is a MyhillNerode theorem for infinite alphabets. We consider several kinds of those: alphabets whose letters can be compared only for equality, but also ones with more structure, such as a total order or a partial order. We develop a framework for studying such alp ..."
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Cited by 17 (5 self)
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Abstract—Our motivating question is a MyhillNerode theorem for infinite alphabets. We consider several kinds of those: alphabets whose letters can be compared only for equality, but also ones with more structure, such as a total order or a partial order. We develop a framework for studying such alphabets, where the key role is played by the automorphism group of the alphabet. This framework builds on the idea of nominal sets of Gabbay and Pitts; nominal sets are the special case of our framework where letters can be only compared for equality. We use the framework to uniformly generalize to infinite alphabets parts of automata theory, including decidability results. In the case of letters compared for equality, we obtain automata equivalent in expressive power to finite memory automata, as defined by Francez and Kaminski. I.
Towards Nominal Computation
, 2012
"... Nominal sets are a different kind of set theory, with a more relaxed notion of finiteness. They offer an elegant formalism for describing λterms modulo αconversion, or automata on data words. This paper is an attempt at defining computation in nominal sets. We present a rudimentary programming lan ..."
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Cited by 10 (4 self)
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Nominal sets are a different kind of set theory, with a more relaxed notion of finiteness. They offer an elegant formalism for describing λterms modulo αconversion, or automata on data words. This paper is an attempt at defining computation in nominal sets. We present a rudimentary programming language, called Nλ. The key idea is that it includes a native type for finite sets in the nominal sense. To illustrate the power of our language, we write short programs that process automata on data words.
A graphical representation for the stochastic picalculus
 In Proceedings of Bioconcur’05
, 2005
"... Abstract. This paper presents a graphical representation for the stochastic picalculus, which builds on previous formal and informal notations. The graphical representation is used to model a Mapk signalling cascade and an evolved gene network. One of the main benefits of the representation is its ..."
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Cited by 8 (1 self)
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Abstract. This paper presents a graphical representation for the stochastic picalculus, which builds on previous formal and informal notations. The graphical representation is used to model a Mapk signalling cascade and an evolved gene network. One of the main benefits of the representation is its ability to clearly highlight the existence of cycles, which are a key aspect of many biological systems. Another advantage is its ability to animate interactions between biological system components, in order to clarify the overall system function. The paper also shows how the graphical representation can be used as a front end to a stochastic simulator for the picalculus, in order to allow the direct simulation of graphical models. This complements the existing textual interface of the simulator, with a view to making modelling and simulation of biological systems more accessible to non computer scientists. 1
Model checking usage policies
, 2008
"... We propose a model for specifying, analysing and enforcing safe usage of resources. Our usage policies allow for parametricity over resources, and they can be enforced through finite state automata. The patterns of resource access and creation are described through a basic calculus of usages. In spi ..."
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Cited by 5 (3 self)
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We propose a model for specifying, analysing and enforcing safe usage of resources. Our usage policies allow for parametricity over resources, and they can be enforced through finite state automata. The patterns of resource access and creation are described through a basic calculus of usages. In spite of the augmented flexibility given by resource creation and by policy parametrization, we devise an efficient (polynomialtime) modelchecking technique for deciding when a usage is resourcesafe, i.e. when it complies with all the relevant usage policies.
Events, Causality and Symmetry
, 2008
"... The article discusses causal models, such as Petri nets and event structures, how they have been rediscovered in a wide variety of recent applications, and why they are fundamental to computer science. A discussion of their present limitations leads to their extension with symmetry. The consequences ..."
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Cited by 4 (2 self)
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The article discusses causal models, such as Petri nets and event structures, how they have been rediscovered in a wide variety of recent applications, and why they are fundamental to computer science. A discussion of their present limitations leads to their extension with symmetry. The consequences, actual and potential, are discussed.
Analysis of deadlocks in object groups
 In FMOODS/FORTE
, 2011
"... Abstract. Object groups are collections of objects that perform collective work. We study a calculus with object groups and develop a descriptions of method’s behaviours. 1 ..."
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Cited by 4 (3 self)
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Abstract. Object groups are collections of objects that perform collective work. We study a calculus with object groups and develop a descriptions of method’s behaviours. 1
Automata theory in nominal sets
, 2012
"... Abstract. We study languages over infinite alphabets equipped with some structure that can be tested by recognizing automata. We develop a framework for studying such alphabets and the ensuing automata theory, where the key role is played by an automorphism group of the alphabet. In the process, we ..."
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Cited by 2 (1 self)
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Abstract. We study languages over infinite alphabets equipped with some structure that can be tested by recognizing automata. We develop a framework for studying such alphabets and the ensuing automata theory, where the key role is played by an automorphism group of the alphabet. In the process, we generalize nominal sets due to Gabbay and Pitts.
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.
Thesis description: Namepassing process calculi: operational models and structural operational semantics.
"... My thesis is about foundations for formal semantics of namepassing process calculi. These calculi are languages for describing systems of agents that communicate channel names along named channels. This facility provides a natural way of describing the mobility of communication links. (The πcalcul ..."
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My thesis is about foundations for formal semantics of namepassing process calculi. These calculi are languages for describing systems of agents that communicate channel names along named channels. This facility provides a natural way of describing the mobility of communication links. (The πcalculus of Milner et al. [1992] is a paradigmatic example of such a language.) The thesis is split into two parts, reflecting the two aspects of the foundations of namepassing calculi that are addressed. • Part I of the thesis is dedicated to operational models for namepassing calculi. Conventional operational models, such as labelled transition systems, are inappropriate for namepassing systems. For this reason I develop and relate two different models of namepassing from the literature: indexed labelled transition systems, based on work of Cattani and Sewell [2004], and a coalgebraic approach introduced by Fiore and Turi [2001]. Connections are made with the History Dependent Automata of Montanari and Pistore [2005], and I introduce a new operational model using the nominal logic of Pitts [2003]. • Part II of the thesis concerns structural operational semantics for namepassing calculi. Various work has been done on the meaning of rulebased transition system specifications, and on