IST Austria Thesis

Motivated by the analysis of highly dynamic message-passing systems, i.e. unbounded thread creation, mobility, etc. we present a framework for the analysis of depth-bounded systems. Depth-bounded systems are one of the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. Even though they are infinite state systems depth-bounded systems are well-structured, thus can be analyzed algorithmically. We give an interpretation of depth-bounded systems as graph-rewriting systems. This gives more flexibility and ease of use to apply depth-bounded systems to other type of systems like shared memory concurrency. First, we develop an adequate domain of limits for depth-bounded systems, a prerequisite for the effective representation of downward-closed sets. Downward-closed sets are needed by forward saturation-based algorithms to represent potentially infinite sets of states. Then, we present an abstract interpretation framework to compute the covering set of well-structured transition systems. Because, in general, the covering set is not computable, our abstraction over-approximates the actual covering set. Our abstraction captures the essence of acceleration based-algorithms while giving up enough precision to ensure convergence. We have implemented the analysis in the PICASSO tool and show that it is accurate in practice. Finally, we build some further analyses like termination using the covering set as starting point

Applications of Petri nets

Thesis (Master)--Izmir Institute of Technology, Mathematics, Izmir, 2008Includes bibliographical references (leaves: 51-52)Text in English; Abstract: Turkish and Englishix, 52 leavesPetri nets are powerful formalism for modeling a wide range of dynamic systems and system behaviors. This thesis surveys the basic concept and application of Petri nets. The structure of Petri nets, their marking and execution and several examples of Petri net modeling. In this thesis we research into the analysis of Petri nets. Also we give the structure of Reachability graphs of Petri nets and their advantages for analyzing the Petri nets. The reachability problem for Petri nets is the problem of finding if Mn 2 R(M0) for a given marking Mn in a net (N,M0).We present several different kinds of Petri nets, together with computer tools based on Mathematica. We give the Mathematica commands for Reachability problem and also we created Mathematica commands for Incidence matrix of Petri nets. We study the concept of Petri nets and applications of Petri nets.We especially focus on Biological applications on Petri nets and we work on modeling of Hashimoto.s Thyroiditis in Petri Nets

SIMULATION AND ANALYSIS OF PENTOSE PHOSPHATE PATHWAY IN PLASMODIUM FALCIPARUM USING COLORED PETRI NETS MODEL

Plasmodium falciparum is a protozoan parasite and the deadliest of five human malaria species which is responsible for the majority of malaria related deaths in humans. The erythrocytes’ stage of Plasmodium falciparum depend on Pentose Pathway as an alternative source of energy and it releases electrons used in protecting the Plasmodium falciparum from its host. Colored Petri Net has been recognized as one of the important models in modelling and analyzing biological pathways. It is an accurate qualitative and quantitative modelling tool for modeling complex biological systems. In this work, the modeling of the pentose phosphate pathway in Plasmodium falciparum is presented using the Petri Net Markup Language (PNML). The Colored Petri Net (CPN) models based on the Petri Net representation and the conservation and kinetic equations were used to examine the dynamic behavior of the metabolic pathway. The usefulness of Petri Nets is demonstrated for the quantitative analysis of the pathway. We obtained data from Biocyc database. The constructed model was viewed through the Colored Petri Net Tool (CPN tool 4.0). Specific drug targets called the essential reactions within the pathway were identified, listed and proposed. These essential reactions would alter the functioning of the pathway which would affect the energy and protection needs of the parasite therefore leading to the death of the parasite in the human red blood cell

Structural Invariants for the Verification of Systems with Parameterized Architectures

We consider parameterized concurrent systems consisting of a finite but unknown number of components, obtained by replicating a given set of finite state automata. Components communicate by executing atomic interactions whose participants update their states simultaneously. We introduce an interaction logic to specify both the type of interactions (e.g.\ rendez-vous, broadcast) and the topology of the system (e.g.\ pipeline, ring). The logic can be easily embedded in monadic second order logic of finitely many successors, and is therefore decidable. Proving safety properties of such a parameterized system, like deadlock freedom or mutual exclusion, requires to infer an inductive invariant that contains all reachable states of all system instances, and no unsafe state. We present a method to automatically synthesize inductive invariants directly from the formula describing the interactions, without costly fixed point iterations. We experimentally prove that this invariant is strong enough to verify safety properties of a large number of systems including textbook examples (dining philosophers, synchronization schemes), classical mutual exclusion algorithms, cache-coherence protocols and self-stabilization algorithms, for an arbitrary number of components.Comment: preprint; to be published in the proceedings of TACAS2

A graphical environment and applications for discrete event and hybrid systems in robotics and automation

technical reportIn this paper we present an overview for the development of a graphical environment for simulating, analyzing, synthesizing, monitoring, and controlling complex discrete event and hybrid systems within the robotics, automation, and intelligent system domain. We start by presenting an overview of discrete event and hybrid systems, and then discuss the proposed framework. We also present two applications within the robotics and automation domain for such complex systems. The first is for formulating an observer for manipulating agents, and the second is for designing sensing strategies for the inspection of machine parts

Analysing Coloured Petri Nets by the Occurrence Graph Method

This paper provides an overview og the work done for the author's PhD thesis. The research area of Coloured Petri Nets is introduced, and the available analysis methods are presented. The occurrence graph method, which is the main subject of this thesis, is described in more detail. Summaries of the six papers which, together with this overview, comprise the thesis are given, and the contributions are discussed.A large portion of this overview is dedicated to a description of related work. The aim is twofold: First, to survey pertinent results within the research areas of -- in increasing generality -- Coloured Petri Nets, High-level Petri Nets, and formalisms for modelling and analysis of parallel and distributed systems. Second, to put the results obtained in this thesis in a wider perspective by comparing them with important related work