Petri net modules in the transformation-based component framework

AbstractComponent-based software engineering needs to be backed by thorough formal concepts and modeling techniques. This paper combines two concepts introduced independently by the two authors in previous papers. On one hand, the concept of Petri net modules introduced at IDPT 2002 in Padberg [J. Padberg, Petri net modules, Journal on Integrated Design and Process Technology 6 (4) (2002) 105–120], and on the other hand a generic component framework for system modeling introduced at FASE 2002 in Ehrig et al. [H. Ehrig, F. Orejas, B. Braatz, M. Klein, M. Piirainen, A generic component concept for system modeling, in: Proceedings of FASE ’02, Lecture Notes in Computer Science, vol. 2306, Springer, 2002]. First we develop a categorical formalization of the transformation based approach to components that is based on pushouts. This is the frame in which we show that Petri net modules can be considered as an instantiation of the generic component framework. This allows applying the transformation based semantics and compositionality result of the generic framework to Petri net modules. In addition to general Petri net modules we introduce Petri net modules preserving safety properties which can be considered as another instantiation of pushout based formalization of the generic framework

Construction and Analysis of Petri Net Model for Distributed Cyber Physical Systems

A Distributed Cyber-Physical System (DCPS) composition poses challenges in determining its emergent behaviour. These challenges occur due to (1) the appearance of causal loops of information and energy flow through cyber and physical channels and (2) inherent non-determinism in the temporally ordered flow of events within independently evolving interacting processes of Constituent Systems (CSs). Hence, there is a need to construct a model of the envisaged schematic of DCPS composition for analysis and verification of its significant properties in the conceptual design stage of the system development life cycle. This paper presents a procedure to construct DCPS composition models in Petri net formalism using distributed abstractions. The model for each CS is obtained from elementary constructs using compositional operators. The interaction among CSs occurs through channels obtained by connecting send and receive constructs of two CSs participating in an interaction. The internal processing within a CS characterizing its primary function is abstracted in a generic passthrough construct. Representing these constructs with compositional operators results in the complete DCPS model in Petri net formalism. A toolchain with Reference net workshop (Renew) as an integrated Petri net editing and analysis platform is configured to support DCPS modelling, simulation and analysis. The Renew tool functionality has been enhanced with a plugin designed and developed by authors to facilitate the drawing of the distributed composition model. A low-level Petri net analysis (Lola) v2.0 plugin is employed to verify the Petri net and temporal properties of the modelled DCPS scenarios. The properties of the resultant model are verified using well-established algorithms to analyze Petri nets. Further, system properties specified using temporal logic can be verified using model-checking algorithms for Petri nets. A moderately complex scenario involving interactions among six CSs illustrates the presented approach

Structural Translation of Time Petri Nets into Timed Automata

International audienceIn this paper, we consider Time Petri Nets (TPN) where time is associated with transitions. We give a formal semantics for TPNs in terms of Timed Transition Systems. Then, we propose a translation from TPNs to Timed Automata (TA) that preserves the behavioural semantics (timed bisimilarity) of the TPNs. For the theory of TPNs this result is two-fold: i) reachability problems and more generally TCTL model-checking are decidable for bounded TPNs; ii) allowing strict time constraints on transitions for TPNs preserves the results described in i). The practical applications of the translation are: i) one can specify a system using both TPNs and Timed Automata and a precise semantics is given to the composition; ii) one can use existing tools for analysing timed automata (like KRONOS or UPPAAL or CMC) to analyse TPNs

Structural translation from time petri nets to timed automata

International audienceIn this paper, we consider Time Petri Nets (TPN) where time is associated with transitions. We give a formal semantics for TPNs in terms of Timed Transition Systems. Then, we propose a translation from TPNs to Timed Automata (TA) that preserves the behavioral semantics (timed bisimilarity) of the TPNs. For the theory of TPNs this result is two-fold: i) reachability problems and more generally TCTL model-checking are decidable for bounded TPNs; ii) allowing strict time constraints on transitions for TPNs preserves the results described in i). The practical appli- cations of the translation are: i) one can specify a system using both TPNs and Timed Automata and a precise semantics is given to the composition; ii) one can use existing tools for analyzing timed automata (like Kronos, Uppaal or Cmc) to analyze TPNs. In this paper we describe the new feature of the tool Romeo that implements our translation of TPNs in the Uppaal input format. We also report on experiments carried out on various examples and compare the result of our method to state-of-the-art tool for analyzing TPNs

Process versus Unfolding Semantics for Place/Transition Petri Nets

In the last few years, the semantics of Petri nets has been investigated in several different ways. Apart from the classical "token game," one can model the behaviour of Petri nets via non-sequential processes, via unfolding constructions, which provide formal relationships between nets and domains, and via algebraic models, which view Petri nets as essentially algebraic theories whose models are monoidal categories. In this paper we show that these three points of view can be reconciled. In our formal development a relevant role is played by DecOcc, a category of occurrence nets appropriately decorated to take into account the history of tokens. The structure of decorated occurrence nets at the same time provides natural unfoldings for Place/Transition (PT) nets and suggests a new notion of processes, the decorated processes, which induce on Petri nets the same semantics as that of unfolding. In addition, we prove that the decorated processes of a net can be axiomatized as the arrows of a symmetric monoidal category which, therefore, provides the aforesaid unification

Compositional approach to design of digital circuits

PhD ThesisIn this work we explore compositional methods for design of digital circuits with the aim of improving existing methodoligies for desigh reuse. We address compositionality techniques looking from both structural and behavioural perspectives. First we consider the existing method of handshake circuit optimisation via control path resynthesis using Petri nets, an approach using structural composition. In that approach labelled Petri net parallel composition plays an important role and we introduce an improvement to the parallel composition algorithm, reducing the number of redundant places in the resulting Petri net representations. The proposed algorithm applies to labelled Petri nets in general and can be applied outside of the handshake circuit optimisation use case. Next we look at the conditional partial order graph (CPOG) formalism, an approach that allows for a convenient representation of systems consisting of multiple alternative system behaviours, a phenomenon we call behavioural composition. We generalise the notion of CPOG and identify an algebraic structure on a more general notion of parameterised graph. This allows us to do equivalence-preserving manipulation of graphs in symbolic form, which simplifies specification and reasoning about systems defined in this way, as displayed by two case studies. As a third contribution we build upon the previous work of CPOG synthesis used to generate binary encoding of microcontroller instruction sets and design the corresponding instruction decoder logic. The proposed CPOG synthesis technique solves the optimisation problem for the general case, reducing it to Boolean satisfiability problem and uses existing SAT solving tools to obtain the result.This work was supported by a studentship from Newcastle University EECE school, EPSRC grant EP/G037809/1 (VERDAD) and EPSRC grant EP/K001698/1 (UNCOVER). i

Verifying chemical reaction network implementations: A pathway decomposition approach

The emerging fields of genetic engineering, synthetic biology, DNA computing, DNA nanotechnology, and molecular programming herald the birth of a new information technology that acquires information by directly sensing molecules within a chemical environment, stores information in molecules such as DNA, RNA, and proteins, processes that information by means of chemical and biochemical transformations, and uses that information to direct the manipulation of matter at the nanometer scale. To scale up beyond current proof-of-principle demonstrations, new methods for managing the complexity of designed molecular systems will need to be developed. Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed “soup” of molecules is stochastic, asynchronous, concurrent, and often involves multiple intermediate steps in the implementation, parallel pathways, and side reactions. This problem relates to the verification of Petri nets, but existing approaches are not sufficient for providing a single guarantee covering an infinite set of possible initial states (molecule counts) and an infinite state space potentially explored by the system given any initial state. We address these issues by formulating a new theory of pathway decomposition that provides an elegant formal basis for comparing chemical reaction network implementations, and we present an algorithm that computes this basis. Our theory naturally handles certain situations that commonly arise in molecular implementations, such as what we call “delayed choice,” that are not easily accommodated by other approaches. We further show how pathway decomposition can be combined with weak bisimulation to handle a wider class that includes most currently known enzyme-free DNA implementation techniques. We anticipate that our notion of logical equivalence between chemical reaction network implementations will be valuable for other molecular implementations such as biochemical enzyme systems, and perhaps even more broadly in concurrency theory

Static Analysis of Deterministic Negotiations

Negotiation diagrams are a model of concurrent computation akin to workflow Petri nets. Deterministic negotiation diagrams, equivalent to the much studied and used free-choice workflow Petri nets, are surprisingly amenable to verification. Soundness (a property close to deadlock-freedom) can be decided in PTIME. Further, other fundamental questions like computing summaries or the expected cost, can also be solved in PTIME for sound deterministic negotiation diagrams, while they are PSPACE-complete in the general case. In this paper we generalize and explain these results. We extend the classical "meet-over-all-paths" (MOP) formulation of static analysis problems to our concurrent setting, and introduce Mazurkiewicz-invariant analysis problems, which encompass the questions above and new ones. We show that any Mazurkiewicz-invariant analysis problem can be solved in PTIME for sound deterministic negotiations whenever it is in PTIME for sequential flow-graphs---even though the flow-graph of a deterministic negotiation diagram can be exponentially larger than the diagram itself. This gives a common explanation to the low-complexity of all the analysis questions studied so far. Finally, we show that classical gen/kill analyses are also an instance of our framework, and obtain a PTIME algorithm for detecting anti-patterns in free-choice workflow Petri nets. Our result is based on a novel decomposition theorem, of independent interest, showing that sound deterministic negotiation diagrams can be hierarchically decomposed into (possibly overlapping) smaller sound diagrams.Comment: To appear in the Proceedings of LICS 2017, IEEE Computer Societ