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

Finite petri nets as models for recursive causal behaviour

Goltz (1988) discussed whether or not there exist finite Petri nets (with unbounded capacities) modelling the causal behaviour of certain recursive CCS terms. As a representative example, the following term is considered: \ud \ud B=(a.nilb.B)+c.nil. \ud \ud We will show that the answer depends on the chosen notion of behaviour. It was already known that the interleaving behaviour and the branching structure of terms as B can be modelled as long as causality is not taken into account. We now show that also the causal behaviour of B can be modelled as long as the branching structure is not taken into account. However, it is not possible to represent both causal dependencies and the behaviour with respect to choices between alternatives in a finite net. We prove that there exists no finite Petri net modelling B with respect to both pomset trace equivalence and failure equivalence

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

Petri Nets and Other Models of Concurrency

This paper retraces, collects, and summarises contributions of the authors --- in collaboration with others --- on the theme of Petri nets and their categorical relationships to other models of concurrency

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

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

On the Model of Computation of 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. More precisely, we introduce the new notion of decorated processes of Petri nets and we show that they induce on nets the same semantics as that of unfolding. In addition, we prove that the decorated processes of a net N can be axiomatized as the arrows of a symmetric monoidal category which, therefore, provides the aforesaid unification

Flux Analysis in Process Models via Causality

We present an approach for flux analysis in process algebra models of biological systems. We perceive flux as the flow of resources in stochastic simulations. We resort to an established correspondence between event structures, a broadly recognised model of concurrency, and state transitions of process models, seen as Petri nets. We show that we can this way extract the causal resource dependencies in simulations between individual state transitions as partial orders of events. We propose transformations on the partial orders that provide means for further analysis, and introduce a software tool, which implements these ideas. By means of an example of a published model of the Rho GTP-binding proteins, we argue that this approach can provide the substitute for flux analysis techniques on ordinary differential equation models within the stochastic setting of process algebras

Axiomatizing Petri Net Concatenable Processes

The concatenable processes of a Petri net $N$ can be characterized abstractly as the arrows of a symmetric monoidal category $P[N]$. Yet, this is only a partial axiomatization, since $P[N]$ is built on a concrete, ad hoc chosen, category of symmetries. In this paper we give a fully equational description of the category of concatenable processes of $N$, thus yielding an axiomatic theory of the noninterleaving behaviour of Petri nets

Reconfigurable Decorated PT Nets with Inhibitor Arcs and Transition Priorities

In this paper we deal with additional control structures for decorated PT Nets. The main contribution are inhibitor arcs and priorities. The first ensure that a marking can inhibit the firing of a transition. Inhibitor arcs force that the transition may only fire when the place is empty. an order of transitions restrict the firing, so that an transition may fire only if it has the highest priority of all enabled transitions. This concept is shown to be compatible with reconfigurable Petri nets