A modular, qualitative modelling of regulatory networks using Petri nets

International audienceAdvances in high-throughput technologies have enabled the de-lineation of large networks of interactions that control cellular processes. To understand behavioural properties of these complex networks, mathematical and computational tools are required. The multi-valued logical formalism, initially defined by R. Thomas and co-workers, proved well adapted to account for the qualitative knowledge available on regulatory interactions, and also to perform analyses of their dynamical properties. In this context, we present two representations of logical models in terms of Petri nets. In a first step, we briefly show how logical models of regulatory networks can be transposed into standard (place/transition) Petri nets, and discuss the capabilities of such representation. In the second part, we focus on logical regulatory modules and their composition, demonstrating that a high-level Petri net representation greatly facilitates the modelling of interconnected modules. Doing so, we introduce an explicit means to integrate signals from various interconnected modules, taking into account their spatial distribution. This provides a flexible modelling framework to handle regulatory networks that operate at both intra-and intercellular levels. As an illustration, we describe a simplified model of the segment-polarity module involved in the segmentation of the Drosophila embryo

Feature Nets: behavioural modelling of software product lines

Software product lines (SPL) are diverse systems that are developed using a dual engineering process: (a)family engineering defines the commonality and variability among all members of the SPL, and (b) application engineering derives specific products based on the common foundation combined with a variable selection of features. The number of derivable products in an SPL can thus be exponential in the number of features. This inherent complexity poses two main challenges when it comes to modelling: Firstly, the formalism used for modelling SPLs needs to be modular and scalable. Secondly, it should ensure that all products behave correctly by providing the ability to analyse and verify complex models efficiently. In this paper we propose to integrate an established modelling formalism (Petri nets) with the domain of software product line engineering. To this end we extend Petri nets to Feature Nets. While Petri nets provide a framework for formally modelling and verifying single software systems, Feature Nets offer the same sort of benefits for software product lines. We show how SPLs can be modelled in an incremental, modular fashion using Feature Nets, provide a Feature Nets variant that supports modelling dynamic SPLs, and propose an analysis method for SPL modelled as Feature Nets. By facilitating the construction of a single model that includes the various behaviours exhibited by the products in an SPL, we make a significant step towards efficient and practical quality assurance methods for software product lines

Abridged Petri Nets

A new graphical framework, Abridged Petri Nets (APNs) is introduced for bottom-up modeling of complex stochastic systems. APNs are similar to Stochastic Petri Nets (SPNs) in as much as they both rely on component-based representation of system state space, in contrast to Markov chains that explicitly model the states of an entire system. In both frameworks, so-called tokens (denoted as small circles) represent individual entities comprising the system; however, SPN graphs contain two distinct types of nodes (called places and transitions) with transitions serving the purpose of routing tokens among places. As a result, a pair of place nodes in SPNs can be linked to each other only via a transient stop, a transition node. In contrast, APN graphs link place nodes directly by arcs (transitions), similar to state space diagrams for Markov chains, and separate transition nodes are not needed. Tokens in APN are distinct and have labels that can assume both discrete values ("colors") and continuous values ("ages"), both of which can change during simulation. Component interactions are modeled in APNs using triggers, which are either inhibitors or enablers (the inhibitors' opposites). Hierarchical construction of APNs rely on using stacks (layers) of submodels with automatically matching color policies. As a result, APNs provide at least the same modeling power as SPNs, but, as demonstrated by means of several examples, the resulting models are often more compact and transparent, therefore facilitating more efficient performance evaluation of complex systems.Comment: 17 figure

The Impact of Petri Nets on System-of-Systems Engineering

The successful engineering of a large-scale system-of-systems project towards deterministic behaviour depends on integrating autonomous components using international communications standards in accordance with dynamic requirements. To-date, their engineering has been unsuccessful: no combination of top-down and bottom-up engineering perspectives is adopted, and information exchange protocol and interfaces between components are not being precisely specified. Various approaches such as modelling, and architecture frameworks make positive contributions to system-of-systems specification but their successful implementation is still a problem. One of the most popular modelling notations available for specifying systems, UML, is intuitive and graphical but also ambiguous and imprecise. Supplying a range of diagrams to represent a system under development, UML lacks simulation and exhaustive verification capability. This shortfall in UML has received little attention in the context of system-of-systems and there are two major research issues: 1. Where the dynamic, behavioural diagrams of UML can and cannot be used to model and analyse system-of-systems 2. Determining how Petri nets can be used to improve the specification and analysis of the dynamic model of a system-of-systems specified using UML This thesis presents the strengths and weaknesses of Petri nets in relation to the specification of system-of-systems and shows how Petri net models can be used instead of conventional UML Activity Diagrams. The model of the system-of-systems can then be analysed and verified using Petri net theory. The Petri net formalism of behaviour is demonstrated using two case studies from the military domain. The first case study uses Petri nets to specify and analyse a close air support mission. This case study concludes by indicating the strengths, weaknesses, and shortfalls of the proposed formalism in system-of-systems specification. The second case study considers specification of a military exchange network parameters problem and the results are compared with the strengths and weaknesses identified in the first case study. Finally, the results of the research are formulated in the form of a Petri net enhancement to UML (mapping existing activity diagram elements to Petri net elements) to meet the needs of system-of-systems specification, verification and validation

A Modular Integrated Development Environment for Coloured Petri Net Models

Distributed software systems are becoming increasingly popular and used. Most of modern distributed systems provide the application of concurrency, also in- cluding resource sharing, communication and synchronization between different modules. These distributed systems comes with the challenges concerning data synchronization, scalability and performance, among others. By modelling these systems helps with solving these challenges, and there exists multiple tools for this. CPN Tools is one of these tools. CPN Tools is used for editing, simulating and analyzing Coloured Petri nets models. A need has been identified to devel- oped new software for develop new and up to date tools for editing, simulating and analyzing Coloured Petri nets to further development and fit the increasing need for distributed systems. Answering this need, a new simulating tool has been proposed. This thesis proposes an editor focusing on the modelling and visualization with the potentially integrate this simulator. This editor consists of an application running on Electron and using GoJS for modelling. This has resulted in a modelling tool for creating CPN models, with the possibility of increased abstraction of the models of the modern distributed systems.Masteroppgave i Programvareutvikling samarbeid med HVLPROG399MAMN-PRO

A Polynomial Translation of pi-calculus FCPs to Safe Petri Nets

We develop a polynomial translation from finite control pi-calculus processes to safe low-level Petri nets. To our knowledge, this is the first such translation. It is natural in that there is a close correspondence between the control flows, enjoys a bisimulation result, and is suitable for practical model checking.Comment: To appear in special issue on best papers of CONCUR'12 of Logical Methods in Computer Scienc

On functional module detection in metabolic networks

Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided identification of functional modules becomes more and more important. Since steady states play a key role in biology, many methods have been developed in that context, for example, elementary flux modes, extreme pathways, transition invariants and place invariants. Metabolic networks can be studied also from the point of view of graph theory, and algorithms for graph decomposition have been applied for the identification of functional modules. A prominent and currently intensively discussed field of methods in graph theory addresses the Q-modularity. In this paper, we recall known concepts of module detection based on the steady-state assumption, focusing on transition-invariants (elementary modes) and their computation as minimal solutions of systems of Diophantine equations. We present the Fourier-Motzkin algorithm in detail. Afterwards, we introduce the Q-modularity as an example for a useful non-steady-state method and its application to metabolic networks. To illustrate and discuss the concepts of invariants and Q-modularity, we apply a part of the central carbon metabolism in potato tubers (Solanum tuberosum) as running example. The intention of the paper is to give a compact presentation of known steady-state concepts from a graph-theoretical viewpoint in the context of network decomposition and reduction and to introduce the application of Q-modularity to metabolic Petri net models

Representing Conversations for Scalable Overhearing

Open distributed multi-agent systems are gaining interest in the academic community and in industry. In such open settings, agents are often coordinated using standardized agent conversation protocols. The representation of such protocols (for analysis, validation, monitoring, etc) is an important aspect of multi-agent applications. Recently, Petri nets have been shown to be an interesting approach to such representation, and radically different approaches using Petri nets have been proposed. However, their relative strengths and weaknesses have not been examined. Moreover, their scalability and suitability for different tasks have not been addressed. This paper addresses both these challenges. First, we analyze existing Petri net representations in terms of their scalability and appropriateness for overhearing, an important task in monitoring open multi-agent systems. Then, building on the insights gained, we introduce a novel representation using Colored Petri nets that explicitly represent legal joint conversation states and messages. This representation approach offers significant improvements in scalability and is particularly suitable for overhearing. Furthermore, we show that this new representation offers a comprehensive coverage of all conversation features of FIPA conversation standards. We also present a procedure for transforming AUML conversation protocol diagrams (a standard human-readable representation), to our Colored Petri net representation