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

Matrix-geometric solution of infinite stochastic Petri nets

We characterize a class of stochastic Petri nets that can be solved using matrix geometric techniques. Advantages of such on approach are that very efficient mathematical technique become available for practical usage, as well as that the problem of large state spaces can be circumvented. We first characterize the class of stochastic Petri nets of interest by formally defining a number of constraints that have to be fulfilled. We then discuss the matrix geometric solution technique that can be employed and present some boundary conditions on tool support. We illustrate the practical usage of the class of stochastic Petri nets with two examples: a queueing system with delayed service and a model of connection management in ATM network

Quantitative evaluation of Pandora Temporal Fault Trees via Petri Nets

© 2015, IFAC (International Federation of Automatic Control) Hosting by Elsevier Ltd. All rights reserved. Using classical combinatorial fault trees, analysts are able to assess the effects of combinations of failures on system behaviour but are unable to capture sequence dependent dynamic behaviour. Pandora introduces temporal gates and temporal laws to fault trees to allow sequence-dependent dynamic analysis of events. Pandora can be easily integrated in model-based design and analysis techniques; however, the combinatorial quantification techniques used to solve classical fault trees cannot be applied to temporal fault trees. Temporal fault trees capture state and therefore require a state space solution for quantification of probability. In this paper, we identify Petri Nets as a possible framework for quantifying temporal trees. We describe how Pandora fault trees can be mapped to Petri Nets for dynamic dependability analysis and demonstrate the process on a fault tolerant fuel distribution system model

A Class of Stochastic Petri Nets with Step Semantics and Related Equivalence Notions

This paper presents a class of Stochastic Petri Nets with concurrent transition firings. It is assumed that transitions occur in steps and that for every step each enabled transition decides probabilistically whether it wants to participate in the step or not. Among the transitions which what to participate in a step, a maximal number is chosen to perform the firing step. The observable behavior is defined and equivalence relations are introduced. The equivalence relations extend the well-known trace and bisimulation equivalences for systems with step semantics to Stochastik Petri Nets with concurrent transition firing. It is shown that the equivalence notions form a lattice of interrelations

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

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

Bisimulation Relations Between Automata, Stochastic Differential Equations and Petri Nets

Two formal stochastic models are said to be bisimilar if their solutions as a stochastic process are probabilistically equivalent. Bisimilarity between two stochastic model formalisms means that the strengths of one stochastic model formalism can be used by the other stochastic model formalism. The aim of this paper is to explain bisimilarity relations between stochastic hybrid automata, stochastic differential equations on hybrid space and stochastic hybrid Petri nets. These bisimilarity relations make it possible to combine the formal verification power of automata with the analysis power of stochastic differential equations and the compositional specification power of Petri nets. The relations and their combined strengths are illustrated for an air traffic example.Comment: 15 pages, 4 figures, Workshop on Formal Methods for Aerospace (FMA), EPTCS 20m 201

A case study in model-driven synthetic biology

We report on a case study in synthetic biology, demonstrating the modeldriven design of a self-powering electrochemical biosensor. An essential result of the design process is a general template of a biosensor, which can be instantiated to be adapted to specific pollutants. This template represents a gene expression network extended by metabolic activity. We illustrate the model-based analysis of this template using qualitative, stochastic and continuous Petri nets and related analysis techniques, contributing to a reliable and robust design