Linear logic on Petri nets

This article shows how individual Petri nets form models of Girard's intuitionistic linear logic. It explores questions of expressiveness and completeness of linear logic with respect to this interpretation. An aim is to use Petri nets to give an understanding of linear logic and give some appraisal of the value of linear logic as a specification logic for Petri nets. This article might serve as a tutorial, providing one in-road into Girard's linear logic via Petri nets. With this in mind we have added several exercises and their solutions. We have made no attempt to be exhaustive in our treatment, dedicating our treatment to one semantics of intuitionistic linear logic. Completeness is shown for several versions of Girard's linear logic with respect to Petri nets as the class of models. The strongest logic considered is intuitionistic linear logic, with (*), --, &, (+) and the exponential ! (``of course''), and forms of quantification. This logic is shown sound and complete with respect to atomic nets (these include nets in which every transition leads to a nonempty multiset of places). The logic is remarkably expressive, enabling descriptions of the kinds of properties one might wish to show of nets; in particular, negative properties, asserting the impossibility of an assertion, can also be expressed. A start is made on decidability issues

Completeness Results for Linear Logic on Petri Nets

Completeness is shown for several versions of Girard's linear logic with respect to Petri nets as the class of models. The strongest logic considered is intuitionistic linear logic, with $\otimes$, $-\!\circ$, \&, $\oplus$ and the exponential ! (''of course´´), and forms of quantification. This logic is shown sound and complete with respect to atomic nets (these include nets in which every transition leads to a nonempty multiset of places). The logic is remarkably expressive, enabling descriptions of the kinds of properties one might wish to show of nets; in particular, negative properties, asserting the impossibility of an assertion, can also be expressed

Bounded LTL Model Checking with Stable Models

In this paper bounded model checking of asynchronous concurrent systems is introduced as a promising application area for answer set programming. As the model of asynchronous systems a generalisation of communicating automata, 1-safe Petri nets, are used. It is shown how a 1-safe Petri net and a requirement on the behaviour of the net can be translated into a logic program such that the bounded model checking problem for the net can be solved by computing stable models of the corresponding program. The use of the stable model semantics leads to compact encodings of bounded reachability and deadlock detection tasks as well as the more general problem of bounded model checking of linear temporal logic. Correctness proofs of the devised translations are given, and some experimental results using the translation and the Smodels system are presented.Comment: 32 pages, to appear in Theory and Practice of Logic Programmin

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

Functorial Semantics for Petri Nets under the Individual Token Philosophy

Although the algebraic semantics of place/transition Petri nets under the collective token philosophy has been fully explained in terms of (strictly) symmetric (strict) monoidal categories, the analogous construction under the individual token philosophy is not completely satisfactory because it lacks universality and also functoriality. We introduce the notion of pre-net to recover these aspects, obtaining a fully satisfactory categorical treatment centered on the notion of adjunction. This allows us to present a purely logical description of net behaviours under the individual token philosophy in terms of theories and theory morphisms in partial membership equational logic, yielding a complete match with the theory developed by the authors for the collective token view of net

A Comparison of Petri Net Semantics under the Collective Token Philosophy

In recent years, several semantics for place/transition Petri nets have been proposed that adopt the collective token philosophy. We investigate distinctions and similarities between three such models, namely configuration structures, concurrent transition systems, and (strictly) symmetric (strict) monoidal categories. We use the notion of adjunction to express each connection. We also present a purely logical description of the collective token interpretation of net behaviours in terms of theories and theory morphisms in partial membership equational logic

Analysis of signalling pathways using the prism model checker

We describe a new modelling and analysis approach for signal transduction networks in the presence of incomplete data. We illustrate the approach with an example, the RKIP inhibited ERK pathway [1]. Our models are based on high level descriptions of continuous time Markov chains: reactions are modelled as synchronous processes and 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 of queries such as if a concentration reaches a certain level, will it remain at that level thereafter? 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