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

Tools and Algorithms for the Construction and Analysis of Systems

This book is Open Access under a CC BY licence. The LNCS 11427 and 11428 proceedings set constitutes the proceedings of the 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2019, which took place in Prague, Czech Republic, in April 2019, held as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2019. The total of 42 full and 8 short tool demo papers presented in these volumes was carefully reviewed and selected from 164 submissions. The papers are organized in topical sections as follows: Part I: SAT and SMT, SAT solving and theorem proving; verification and analysis; model checking; tool demo; and machine learning. Part II: concurrent and distributed systems; monitoring and runtime verification; hybrid and stochastic systems; synthesis; symbolic verification; and safety and fault-tolerant systems

Computer Aided Verification

This open access two-volume set LNCS 11561 and 11562 constitutes the refereed proceedings of the 31st International Conference on Computer Aided Verification, CAV 2019, held in New York City, USA, in July 2019. The 52 full papers presented together with 13 tool papers and 2 case studies, were carefully reviewed and selected from 258 submissions. The papers were organized in the following topical sections: Part I: automata and timed systems; security and hyperproperties; synthesis; model checking; cyber-physical systems and machine learning; probabilistic systems, runtime techniques; dynamical, hybrid, and reactive systems; Part II: logics, decision procedures; and solvers; numerical programs; verification; distributed systems and networks; verification and invariants; and concurrency

Quantitative Robustness Analysis of Flat Timed Automata

Whereas formal verification of timed systems has become a very active field of research, the idealized mathematical semantics of timed automata cannot be faithfully implemented. Recently, several works have studied a parametric semantics of timed automata related to implementability: if the specification is met for some positive value of the parameter, then there exists a correct implementation. In addition, the value of the parameter gives lower bounds on sufficient resources for the implementation. In this work, we present a symbolic algorithm for the computation of the parametric reachability set under this semantics for flat timed automata. As a consequence, we can compute the largest value of the parameter for a timed automaton to be safe

Computer Aided Verification

This open access two-volume set LNCS 11561 and 11562 constitutes the refereed proceedings of the 31st International Conference on Computer Aided Verification, CAV 2019, held in New York City, USA, in July 2019. The 52 full papers presented together with 13 tool papers and 2 case studies, were carefully reviewed and selected from 258 submissions. The papers were organized in the following topical sections: Part I: automata and timed systems; security and hyperproperties; synthesis; model checking; cyber-physical systems and machine learning; probabilistic systems, runtime techniques; dynamical, hybrid, and reactive systems; Part II: logics, decision procedures; and solvers; numerical programs; verification; distributed systems and networks; verification and invariants; and concurrency

Contribution to the verification of timed automata (determinization, quantitative verification and reachability in networks of automata)

Cette thèse porte sur la vérification des automates temporisés, un modèle bien établi pour les systèmes temps-réels. La thèse est constituée de trois parties. La première est dédiée à la déterminisation des automates temporisés, problème qui n'a pas de solution en général. Nous proposons une méthode approchée (sur-approximation, sous-approximation, mélange des deux) fondée sur la construction d'un jeu de sûreté. Cette méthode améliore les approches existantes en combinant leurs avantages respectifs. Nous appliquons ensuite cette méthode de déterminisation à la génération automatique de tests de conformité. Dans la seconde partie, nous prenons en compte des aspects quantitatifs des systèmes temps-réel grâce à une notion de fréquence des états acceptants dans une exécution d'un automate temporisé. Plus précisément, la fréquence d'une exécution est la proportion de temps passée dans les états acceptants. Nous intéressons alors à l'ensemble des fréquences des exécutions d'un automate temporisé pour étudier, par exemple, le vide de langages seuils. Nous montrons ainsi que les bornes de l'ensemble des fréquences sont calculables pour deux classes d'automates temporisés. D'une part, les bornes peuvent être calculées en espace logarithmique par une procédure non-déterministe dans les automates temporisés à une horloge. D'autre part, elles peuvent être calculées en espace polynomial dans les automates temporisés à plusieurs horloges ne contenant pas de cycles forçant la convergence d'horloges. Finalement, nous étudions le problème de l'accessibilité des états acceptants dans des réseaux d'automates temporisés qui communiquent via des files FIFO. Nous considérons tout d'abord des automates temporisés à temps discret, et caractérisons les topologies de réseaux pour lesquelles l'accessibilité est décidable. Cette caractérisation est ensuite étendue aux automates temporisés à temps continu.This thesis is about verification of timed automata, a well-established model for real time systems. The document is structured in three parts. The first part is dedicated to the determinization of timed automata, a problem which has no solution in general. We propose an approximate (over-approximation/under-approximation/mix) method based on the construction of a safety game. This method improves both existing approaches by combining their respective advantages. Then, we apply this determinization approach to the generation of conformance tests. In the second part, we take into account quantitative aspects of real time systems thanks to a notion of frequency of accepting states along executions of timed automata. More precisely, the frequency of a run is the proportion of time elapsed in accepting states. Then, we study the set of frequencies of runs of a timed automaton in order to decide, for example, the emptiness of threshold languages. We thus prove that the bounds of the set of frequencies are computable for two classes of timed automata. On the one hand, we prove that bounds are computable in logarithmic space by a non-deterministic procedure in one-clock timed automata. On the other hand, they can be computed in polynomial space in timed automata with several clocks, but having no cycle that forces the convergence between clocks. Finally, we study the reachability problem in networks of timed automata communicating through FIFO channels. We first consider dicrete timed automata, and characterize topologies of networks for which reachability is decidable. Then, this characterization is extended to dense-time automata.RENNES1-Bibl. électronique (352382106) / SudocSudocFranceF