Event structures for Petri nets with persistence

Event structures are a well-accepted model of concurrency. In a seminal paper by Nielsen, Plotkin and Winskel, they are used to establish a bridge between the theory of domains and the approach to concurrency proposed by Petri. A basic role is played by an unfolding construction that maps (safe) Petri nets into a subclass of event structures, called prime event structures, where each event has a uniquely determined set of causes. Prime event structures, in turn, can be identified with their domain of configurations. At a categorical level, this is nicely formalised by Winskel as a chain of coreflections. Contrary to prime event structures, general event structures allow for the presence of disjunctive causes, i.e., events can be enabled by distinct minimal sets of events. In this paper, we extend the connection between Petri nets and event structures in order to include disjunctive causes. In particular, we show that, at the level of nets, disjunctive causes are well accounted for by persistent places. These are places where tokens, once generated, can be used several times without being consumed and where multiple tokens are interpreted collectively, i.e., their histories are inessential. Generalising the work on ordinary nets, Petri nets with persistence are related to a new subclass of general event structures, called locally connected, by means of a chain of coreflections relying on an unfolding construction

Subtyping for Hierarchical, Reconfigurable Petri Nets

Hierarchical Petri nets allow a more abstract view and reconfigurable Petri nets model dynamic structural adaptation. In this contribution we present the combination of reconfigurable Petri nets and hierarchical Petri nets yielding hierarchical structure for reconfigurable Petri nets. Hierarchies are established by substituting transitions by subnets. These subnets are themselves reconfigurable, so they are supplied with their own set of rules. Moreover, global rules that can be applied in all of the net, are provided

Analysis of Petri Nets and Transition Systems

This paper describes a stand-alone, no-frills tool supporting the analysis of (labelled) place/transition Petri nets and the synthesis of labelled transition systems into Petri nets. It is implemented as a collection of independent, dedicated algorithms which have been designed to operate modularly, portably, extensibly, and efficiently.Comment: In Proceedings ICE 2015, arXiv:1508.0459

KReach : a tool for reachability in petri nets

We present KReach, a tool for deciding reachability in general Petri nets. The tool is a full implementation of Kosaraju’s original 1982 decision procedure for reachability in VASS. We believe this to be the first implementation of its kind. We include a comprehensive suite of libraries for development with Vector Addition Systems (with States) in the Haskell programming language. KReach serves as a practical tool, and acts as an effective teaching aid for the theory behind the algorithm. Preliminary tests suggest that there are some classes of Petri nets for which we can quickly show unreachability. In particular, using KReach for coverability problems, by reduction to reachability, is competitive even against state-of-the-art coverability checkers

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways

http://dx.doi.org/10.1093/bib/bbn026Quantitative models of biochemical networks (signal transduction cascades, metabolic pathways, gene regulatory circuits) are a central component of modern systems biology. Building and managing these complex models is a major challenge that can benefit from the application of formal methods adopted from theoretical computing science. Here we provide a general introduction to the field of formal modelling, which emphasizes the intuitive biochemical basis of the modelling process, but is also accessible for an audience with a background in computing science and/or model engineering. We show how signal transduction cascades can be modelled in a modular fashion, using both a qualitative approach { Qualitative Petri nets, and quantitative approaches { Continuous Petri Nets and Ordinary Differential Equations. We review the major elementary building blocks of a cellular signalling model, discuss which critical design decisions have to be made during model building, and present ..

Read Operators and their Expressiveness in Process Algebras

We study two different ways to enhance PAFAS, a process algebra for modelling asynchronous timed concurrent systems, with non-blocking reading actions. We first add reading in the form of a read-action prefix operator. This operator is very flexible, but its somewhat complex semantics requires two types of transition relations. We also present a read-set prefix operator with a simpler semantics, but with syntactic restrictions. We discuss the expressiveness of read prefixes; in particular, we compare them to read-arcs in Petri nets and justify the simple semantics of the second variant by showing that its processes can be translated into processes of the first with timed-bisimilar behaviour. It is still an open problem whether the first algebra is more expressive than the second; we give a number of laws that are interesting in their own right, and can help to find a backward translation.Comment: In Proceedings EXPRESS 2011, arXiv:1108.407

Automating the transformation-based analysis of visual languages

The final publication is available at Springer via http://dx.doi.org/10.1007/s00165-009-0114-yWe present a novel approach for the automatic generation of model-to-model transformations given a description of the operational semantics of the source language in the form of graph transformation rules. The approach is geared to the generation of transformations from Domain-Specific Visual Languages (DSVLs) into semantic domains with an explicit notion of transition, like for example Petri nets. The generated transformation is expressed in the form of operational triple graph grammar rules that transform the static information (initial model) and the dynamics (source rules and their execution control structure). We illustrate these techniques with a DSVL in the domain of production systems, for which we generate a transformation into Petri nets. We also tackle the description of timing aspects in graph transformation rules, and its analysis through their automatic translation into Time Petri netsWork sponsored by the Spanish Ministry of Science and Innovation, project METEORIC (TIN2008-02081/TIN) and by the Canadian Natural Sciences and Engineering Research Council (NSERC)

Membrane Systems with Priority, Dissolution, Promoters and Inhibitors and Time Petri Nets

We continue the investigations on exploring the connection between membrane systems and time Petri nets already commenced in [4] by extending membrane systems with promoters/inhibitors, membrane dissolution and priority for rules compared to the simple symbol-object membrane system. By constructing the simulating Petri net, we retain one of the main characteristics of the Petri net model, namely, the firings of the transitions can take place in any order: we do not impose any additional stipulation on the transition sequences in order to obtain a Petri net model equivalent to the general Turing machine. Instead, we substantially exploit the gain in computational strength obtained by the introduction of the timing feature for Petri nets