TRANSIENT ANALYSIS OF A PREEMPTIVE RESUME M/D/l/2/2 THROUGH PETRI NETS

Stochastic Petri Nets (SPN) are usually designed to support exponential distributions only, with the consequence that their modelling power is restricted to Markovian systems. In recent years, some attempts have appeared in the literature aimed to define SPN models with generally distributed firing times. A particular subclass, called Deterministic and Stochastic Petri Nets (DSPN), combines into a single model both exponential and deterministic transitions. The available DSPN implementations require simplifying assumptions which limit the applicability of the model to preemptive repeat different service mechanisms only. The present paper discusses a semantical generalization of the DSPNs by including preemptive mechanisms of resume type. This generalization is crucial in connection with fault tolerant systems, where the work performed before the interruption should not be lost. By means of this new approach, the transient analysis of a M/D/1/2/2 queue (with 2 customers, 1 server, exponential thinking and deterministic service time) is fully examined under different preemptive resume policies

CSL model checking of Deterministic and Stochastic Petri Nets

Deterministic and Stochastic Petri Nets (DSPNs) are a widely used high-level formalism for modeling discrete-event systems where events may occur either without consuming time, after a deterministic time, or after an exponentially distributed time. The underlying process dened by DSPNs, under certain restrictions, corresponds to a class of Markov Regenerative Stochastic Processes (MRGP). In this paper, we investigate the use of CSL (Continuous Stochastic Logic) to express probabilistic properties, such a time-bounded until and time-bounded next, at the DSPN level. The verication of such properties requires the solution of the steady-state and transient probabilities of the underlying MRGP. We also address a number of semantic issues regarding the application of CSL on MRGP and provide numerical model checking algorithms for this logic. A prototype model checker, based on SPNica, is also described

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Transient analysis of deterministic and stochastic Petri nets with concurrent deterministic transitions

This paper introduces an efficient numerical algorithm for transient analysis of deterministic and stochastic Petri nets (DSPNs) and other discrete-event stochastic systems with exponential and deterministic events. The proposed approach is based on the analysis of a general state space Markov chain (GSSMC) whose state equations constitute a system of multidimensional Fredholm integral equations. Key contributions of this paper constitute the observations that the transition kernel of this system of Fredholm equations is piece-wise continuous and separable. Due to the exploitation of these properties, the GSSMC approach shows great promise for being effectively applicable for the transient analysis of large DSPNs with concurrent deterministic transitions. Moreover, for DSPNs without concurrent deterministic transitions the proposed GSSMC approach requires three orders of magnitude less computational effort than the previously known approach based on the method of supplementary variables

MathMC: A mathematica-based tool for CSL model checking of deterministic and stochastic Petri nets

Deterministic and Stochastic Petri Nets (DSPNs) are a widely used high-level formalism for modeling discreteevent systems where events may occur either without consuming time, after a deterministic time, or after an exponentially distributed time. CSL (Continuous Stochastic Logic) is a (branching) temporal logic developed to express probabilistic properties in continuous time Markov chains (CTMCs). In this paper we present a Mathematica-based tool that implements recent developments for model checking CSL style properties on DSPNs. Furthermore, as a consequence of the type of process underlying DSPNs (a superset of Markovian processes), we are also able to check CSL properties of Generalized Stochastic Petri Nets (GSPNs) and labeled CTMCs

Extension of PRISM by Synthesis of Optimal Timeouts in Fixed-Delay CTMC

We present a practically appealing extension of the probabilistic model checker PRISM rendering it to handle fixed-delay continuous-time Markov chains (fdCTMCs) with rewards, the equivalent formalism to the deterministic and stochastic Petri nets (DSPNs). fdCTMCs allow transitions with fixed-delays (or timeouts) on top of the traditional transitions with exponential rates. Our extension supports an evaluation of expected reward until reaching a given set of target states. The main contribution is that, considering the fixed-delays as parameters, we implemented a synthesis algorithm that computes the epsilon-optimal values of the fixed-delays minimizing the expected reward. We provide a performance evaluation of the synthesis on practical examples

Analysis of signalling pathways using continuous time Markov chains

We describe a quantitative modelling and analysis approach for signal transduction networks. We illustrate the approach with an example, the RKIP inhibited ERK pathway [CSK+03]. Our models are high level descriptions of continuous time Markov chains: proteins are modelled by synchronous processes and reactions by transitions. Concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis such as what is the probability that if a concentration reaches a certain level, it will remain at that level thereafter? or how does varying a given reaction rate affect that probability? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable

Dependability Analysis of Control Systems using SystemC and Statistical Model Checking

Stochastic Petri nets are commonly used for modeling distributed systems in order to study their performance and dependability. This paper proposes a realization of stochastic Petri nets in SystemC for modeling large embedded control systems. Then statistical model checking is used to analyze the dependability of the constructed model. Our verification framework allows users to express a wide range of useful properties to be verified which is illustrated through a case study

Analysis of Petri Net Models through Stochastic Differential Equations

It is well known, mainly because of the work of Kurtz, that density dependent Markov chains can be approximated by sets of ordinary differential equations (ODEs) when their indexing parameter grows very large. This approximation cannot capture the stochastic nature of the process and, consequently, it can provide an erroneous view of the behavior of the Markov chain if the indexing parameter is not sufficiently high. Important phenomena that cannot be revealed include non-negligible variance and bi-modal population distributions. A less-known approximation proposed by Kurtz applies stochastic differential equations (SDEs) and provides information about the stochastic nature of the process. In this paper we apply and extend this diffusion approximation to study stochastic Petri nets. We identify a class of nets whose underlying stochastic process is a density dependent Markov chain whose indexing parameter is a multiplicative constant which identifies the population level expressed by the initial marking and we provide means to automatically construct the associated set of SDEs. Since the diffusion approximation of Kurtz considers the process only up to the time when it first exits an open interval, we extend the approximation by a machinery that mimics the behavior of the Markov chain at the boundary and allows thus to apply the approach to a wider set of problems. The resulting process is of the jump-diffusion type. We illustrate by examples that the jump-diffusion approximation which extends to bounded domains can be much more informative than that based on ODEs as it can provide accurate quantity distributions even when they are multi-modal and even for relatively small population levels. Moreover, we show that the method is faster than simulating the original Markov chain