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49
Stronger computational modelling of signalling pathways using both continuous and discretestate methods
 In To appear in Computational Methods in Systems Biology 2006, LNCS
, 2006
"... Abstract. Starting from a biochemical signalling pathway model expressed in a process algebra enriched with quantitative information we automatically derive both continuousspace and discretestate representations suitable for numerical evaluation. We compare results obtained using implicit numerica ..."
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Cited by 28 (15 self)
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Abstract. Starting from a biochemical signalling pathway model expressed in a process algebra enriched with quantitative information we automatically derive both continuousspace and discretestate representations suitable for numerical evaluation. We compare results obtained using implicit numerical differentiation formulae to those obtained using approximate stochastic simulation thereby exposing a flaw in the use of the differentiation procedure producing misleading results. 1
Structural Operational Semantics for Stochastic Process Calculi
"... Abstract. A syntactic framework called SGSOS, for defining wellbehaved Markovian stochastic transition systems, is introduced by analogy to the GSOS congruence format for nondeterministic processes. Stochastic bisimilarity is guaranteed a congruence for systems defined by SGSOS rules. Associativity ..."
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Cited by 16 (0 self)
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Abstract. A syntactic framework called SGSOS, for defining wellbehaved Markovian stochastic transition systems, is introduced by analogy to the GSOS congruence format for nondeterministic processes. Stochastic bisimilarity is guaranteed a congruence for systems defined by SGSOS rules. Associativity of parallel composition in stochastic process algebras is also studied within the framework. 1
The Measurable Space of Stochastic Processes
, 2013
"... We introduce a stochastic extension of CCS endowed with structural operational semantics expressed in terms of measure theory. The set of processes is organised as a measurable space by the sigmaalgebra generated by structural congruence. The structural operational semantics associates to each pro ..."
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Cited by 14 (5 self)
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We introduce a stochastic extension of CCS endowed with structural operational semantics expressed in terms of measure theory. The set of processes is organised as a measurable space by the sigmaalgebra generated by structural congruence. The structural operational semantics associates to each process a set of measures over the space of processes. The measures encode the rates of the transitions from a process (state of a system) to a measurable set of processes. We prove that stochastic bisimulation is a congruence that extends structural congruence. In addition to an elegant operational semantics, our calculus provides a canonic way to define metrics on processes that measure that measure how similar two processes are in terms of behaviour.
The attributed pi calculus with priorities
 Trans. on Computational Systems Biology
"... HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte p ..."
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Cited by 12 (6 self)
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HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et a ̀ la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
The PEPA Eclipse Plugin
"... The PEPA Eclipse Plugin supports the creation and analysis of performance models from smallscale Markov models to largescale simulation studies and differential equation systems. Whichever form of analysis is used, models are expressed in a single highlevel language for quantitative modelling, Pe ..."
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Cited by 11 (4 self)
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The PEPA Eclipse Plugin supports the creation and analysis of performance models from smallscale Markov models to largescale simulation studies and differential equation systems. Whichever form of analysis is used, models are expressed in a single highlevel language for quantitative modelling, Performance Evaluation Process Algebra (PEPA). 1.
C.: Nondeterminism and Probabilities in Timed Concurrent Constraint Programming
 In: Proc. of ICLP’08. Volume 5366 of LNCS
, 2008
"... We set the grounds of a framework for modeling and verifying systems involving probabilities, time, and partial information as constraints. A timed concurrent constraint process calculus with probabilistic and nondeterministic choices is proposed as description language. An operational semantics ..."
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Cited by 9 (5 self)
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We set the grounds of a framework for modeling and verifying systems involving probabilities, time, and partial information as constraints. A timed concurrent constraint process calculus with probabilistic and nondeterministic choices is proposed as description language. An operational semantics ensures consistent interactions between both kinds of choices. The semantics is also shown to be indispensable for the definition of logicbased verification capabilities over system specifications. The notion of observable behavior of a process –what an environment can perceive from its execution – is shown to provide a unified basis for modeling and reasoning about systems. We illustrate our approach by modeling and verifying a music improvisation scenario. 1
Modular Markovian Logic
"... We introduce Modular Markovian Logic (MML) for compositional continuoustime and continuousspace Markov processes. MML combines operators specific to stochastic logics with operators that reflect the modular structure of the semantics, similar to those used by spatial and separation logics. We pre ..."
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Cited by 9 (7 self)
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We introduce Modular Markovian Logic (MML) for compositional continuoustime and continuousspace Markov processes. MML combines operators specific to stochastic logics with operators that reflect the modular structure of the semantics, similar to those used by spatial and separation logics. We present a complete Hilbertstyle axiomatization for MML, prove the small model property and analyze the relation between the stochastic bisimulation and the logical equivalence relation induced by MML on models.
Ratebased Transition Systems for Stochastic Process Calculi
 AUTOMATA, LANGUAGES AND PROGRAMMING  C. LNCS
, 2009
"... A variant of Rate Transition Systems (RTS), proposed by Klin and Sassone, is introduced and used as the basic model for defining stochastic behaviour of processes. The transition relation used in our variant associates to each process, for each action, the set of possible futures paired with a mea ..."
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Cited by 8 (2 self)
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A variant of Rate Transition Systems (RTS), proposed by Klin and Sassone, is introduced and used as the basic model for defining stochastic behaviour of processes. The transition relation used in our variant associates to each process, for each action, the set of possible futures paired with a measure indicating their rates. We show how RTS can be used for providing the operational semantics of stochastic extensions of three classical formalisms, namely CSP, CCS and picalculus. It is also shown that, in contrast with the original definition by Priami, our semantics for stochastic picalculus guarantees associativity of parallel composition.
Integrated Simulation and ModelChecking for the Analysis of Biochemical Systems
 PASM 2008
, 2008
"... Modelchecking can provide valuable insight into the behaviour of biochemical systems, answering quantitative queries which are more difficult to answer using stochastic simulation alone. However, modelchecking is a computationally intensive technique which can become infeasible if the system under ..."
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Cited by 7 (5 self)
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Modelchecking can provide valuable insight into the behaviour of biochemical systems, answering quantitative queries which are more difficult to answer using stochastic simulation alone. However, modelchecking is a computationally intensive technique which can become infeasible if the system under consideration is too large. Moreover, the finite nature of the state representation used means that a priori bounds must be set for the numbers of molecules of each species to be observed in the system. In this paper we present an approach which addresses these problems by using stochastic simulation and the PRISM model checker in tandem. The stochastic simulation identifies reasonable bounds for molecular populations in the context of the considered experiment. These bounds are used to parameterise the PRISM model and limit its state space. A simulation prerun identifies interesting time intervals on which modelchecking should focus, if this information is not available from experimental data.