Automatic Decomposition of Petri Nets into Automata Networks - A Synthetic Account

International audienceThis article revisits the problem of decomposing a Petri net into a network of automata, a problem that has been around since the early 70s. We reformu-late this problem as the transformation of an ordinary, one-safe Petri net into a flat, unit-safe NUPN (Nested-Unit Petri Net) and define a quality criterion based on the number of bits required for the structural encoding of markings. We propose various transformation methods, all of which we implemented in a tool chain that combines NUPN tools with third-party software, such as SAT solvers, SMT solvers, and tools for graph colouring and finding maximal cliques. We perform an extensive evaluation of these methods on a collection of more than 12,000 nets from diverse sources, including nets whose marking graph is too large for being explored exhaustively

Modeling formalisms in systems biology

Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future.Research supported by grants SFRH/BD/35215/2007 and SFRH/BD/25506/2005 from the Fundacao para a Ciencia e a Tecnologia (FCT) and the MIT-Portugal Program through the project "Bridging Systems and Synthetic Biology for the development of improved microbial cell factories" (MIT-Pt/BS-BB/0082/2008)

Model based fault diagnosis for hybrid systems : application on chemical processes

The complexity and the size of the industrial chemical processes induce the monitoring of a growing number of process variables. Their knowledge is generally based on the measurements of system variables and on the physico-chemical models of the process. Nevertheless, this information is imprecise because of process and measurement noise. So the research ways aim at developing new and more powerful techniques for the detection of process fault. In this work, we present a method for the fault detection based on the comparison between the real system and the reference model evolution generated by the extended Kalman filter. The reference model is simulated by the dynamic hybrid simulator, PrODHyS. It is a general object-oriented environment which provides common and reusable components designed for the development and the management of dynamic simulation of industrial systems. The use of this method is illustrated through a didactic example relating to the field of Chemical Process System Engineering

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

Methodologies synthesis

This deliverable deals with the modelling and analysis of interdependencies between critical infrastructures, focussing attention on two interdependent infrastructures studied in the context of CRUTIAL: the electric power infrastructure and the information infrastructures supporting management, control and maintenance functionality. The main objectives are: 1) investigate the main challenges to be addressed for the analysis and modelling of interdependencies, 2) review the modelling methodologies and tools that can be used to address these challenges and support the evaluation of the impact of interdependencies on the dependability and resilience of the service delivered to the users, and 3) present the preliminary directions investigated so far by the CRUTIAL consortium for describing and modelling interdependencies

Exploring the concept of interaction computing through the discrete algebraic analysis of the Belousov–Zhabotinsky reaction

Interaction computing (IC) aims to map the properties of integrable low-dimensional non-linear dynamical systems to the discrete domain of finite-state automata in an attempt to reproduce in software the self-organizing and dynamically stable properties of sub-cellular biochemical systems. As the work reported in this paper is still at the early stages of theory development it focuses on the analysis of a particularly simple chemical oscillator, the Belousov-Zhabotinsky (BZ) reaction. After retracing the rationale for IC developed over the past several years from the physical, biological, mathematical, and computer science points of view, the paper presents an elementary discussion of the Krohn-Rhodes decomposition of finite-state automata, including the holonomy decomposition of a simple automaton, and of its interpretation as an abstract positional number system. The method is then applied to the analysis of the algebraic properties of discrete finite-state automata derived from a simplified Petri net model of the BZ reaction. In the simplest possible and symmetrical case the corresponding automaton is, not surprisingly, found to contain exclusively cyclic groups. In a second, asymmetrical case, the decomposition is much more complex and includes five different simple non-abelian groups whose potential relevance arises from their ability to encode functionally complete algebras. The possible computational relevance of these findings is discussed and possible conclusions are drawn

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

10231 Abstracts Collection -- Structure Discovery in Biology: Motifs, Networks & Phylogenies

From 06.06. to 11.06.2010, the Dagstuhl Seminar 10231 ``Structure Discovery in Biology: Motifs, Networks & Phylogenies \u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Le jeu de tests VLSAT-2

This report presents VLSAT-2 (an acronym for "Very Large Boolean SATisfiability problems"),the second part of a benchmark suite to be used in scientific experiments and softwarecompetitions addressing SAT-solving issues.VLSAT-2 contains 100 benchmarks (50 satisfiable and 50 unsatisfiable formulas)of increasing complexity, proposed in DIMACS CNF format undera permissive Creative Commons license.25% of these benchmarks have been used during the 2020 and 2021 editionsof the International SAT Competition.VLSAT-2 (acronyme anglais de "très grands problèmes de satisfaisabilité booléenne")est le second volet d'une suite de tests destinée aux expérimentations scientifiqueset aux compétitions de logiciels pour la résolution de problèmes SAT.VLSAT-2 contient 100 tests (50 formules satisfaisables et 50 insatisfaisables)de complexité croissante, fournis en format DIMACS CNF sous une licence Creative Commons permissive.25% de ces tests ont été utilisés lors des éditions 2020 et 2021 de la compétition internationale sur la résolution SAT