Encoding Higher Level Extensions of Petri Nets in Answer Set Programming

Answering realistic questions about biological systems and pathways similar to the ones used by text books to test understanding of students about biological systems is one of our long term research goals. Often these questions require simulation based reasoning. To answer such questions, we need formalisms to build pathway models, add extensions, simulate, and reason with them. We chose Petri Nets and Answer Set Programming (ASP) as suitable formalisms, since Petri Net models are similar to biological pathway diagrams; and ASP provides easy extension and strong reasoning abilities. We found that certain aspects of biological pathways, such as locations and substance types, cannot be represented succinctly using regular Petri Nets. As a result, we need higher level constructs like colored tokens. In this paper, we show how Petri Nets with colored tokens can be encoded in ASP in an intuitive manner, how additional Petri Net extensions can be added by making small code changes, and how this work furthers our long term research goals. Our approach can be adapted to other domains with similar modeling needs

AUTOMATYZACJA SYSTEMOWEGO POZIOMU PROJEKTOWANIA INTELIGENTNEGO DOMU

In the article the smart house (SH) structural scheme, the general performance algorithm of the SH system, and the SH system model based on colored Petri nets, which enables exploring dynamics of the whole system as well as internal interaction of its main structural and functional subsystems at the system level design, have been developed.W artykule przedstawiono opracowanie schematu strukturalnego inteligentnego domu (ID), ogólny algorytm pracy systemu ID, a także model systemu ID na podstawie kolorowej sieci Petri, co pozwala badać dynamikę zachowania zarówno całego systemu ID, jak i wewnętrznego współdziałania jej głównych podsystemów

Timed colored Petri Net generating Arrays

Motivated by Interval Timed Colored Petri Net and two dimensional Array generating Petri nets, this paper defines an Array Generating Timed Colored Petri Net. In this paper time has been associated with the tokens of the net. Time associated with tokens will delay its availability as a resource. The introduction of time as an attribute of the token has an additional control over the firing sequence of the net. The focus of this paper is on the array language generated by such timed colored Petri net model.Publisher's Versio

Petri Nets for Concurrent Programming

Concurrent programming is used in all large and complex computer systems. However, concurrency errors and system failures (ex: crashes and deadlocks) are common. We find that Petri nets can be used to model concurrent systems and find and remove errors ahead of time. We introduce a novel generalization of Petri nets with nondeterministic transition nodes to match real systems. These allow for a compact way to construct, optimize, and prove computer programs at the concurrency level. Petri net programs can also be optimized by automatically solving for maximal concurrency, where the maximum number of valid threads is determined by the structure of the Petri net prior to execution. We discuss an algorithm to compute the state graph of a given Petri net start state pair. We introduce our open source software framework which implements this theory as a general purpose concurrency focused middle-ware

OC-PM: Analyzing Object-Centric Event Logs and Process Models

Object-centric process mining is a novel branch of process mining that aims to analyze event data from mainstream information systems (such as SAP) more naturally, without being forced to form mutually exclusive groups of events with the specification of a case notion. The development of object-centric process mining is related to exploiting object-centric event logs, which includes exploring and filtering the behavior contained in the logs and constructing process models which can encode the behavior of different classes of objects and their interactions (which can be discovered from object-centric event logs). This paper aims to provide a broad look at the exploration and processing of object-centric event logs to discover information related to the lifecycle of the different objects composing the event log. Also, comprehensive tool support (OC-PM) implementing the proposed techniques is described in the paper

Fine-Grained Workflow Interoperability in Life Sciences

In den vergangenen Jahrzehnten führten Fortschritte in den Schlüsseltechnologien der Lebenswissenschaften zu einer exponentiellen Zunahme der zur Verfügung stehenden biologischen Daten. Um Ergebnisse zeitnah generieren zu können werden sowohl spezialisierte Rechensystem als auch Programmierfähigkeiten benötigt: Desktopcomputer oder monolithische Ansätze sind weder in der Lage mit dem Wachstum der verfügbaren biologischen Daten noch mit der Komplexität der Analysetechniken Schritt zu halten. Workflows erlauben diesem Trend durch Parallelisierungsansätzen und verteilten Rechensystemen entgegenzuwirken. Ihre transparenten Abläufe, gegeben durch ihre klar definierten Strukturen, ebenso ihre Wiederholbarkeit, erfüllen die Standards der Reproduzierbarkeit, welche an wissenschaftliche Methoden gestellt werden. Eines der Ziele unserer Arbeit ist es Forschern beim Bedienen von Rechensystemen zu unterstützen, ohne dass Programmierkenntnisse notwendig sind. Dafür wurde eine Sammlung von Tools entwickelt, welche jedes Kommandozeilenprogramm in ein Workflowsystem integrieren kann. Ohne weitere Anpassungen kann unser Programm zwei weit verbreitete Workflowsysteme unterstützen. Unser modularer Entwurf erlaubt zudem Unterstützung für weitere Workflowmaschinen hinzuzufügen. Basierend auf der Bedeutung von frühen und robusten Workflowentwürfen, haben wir außerdem eine wohl etablierte Desktop–basierte Analyseplattform erweitert. Diese enthält über 2.000 Aufgaben, wobei jede als Baustein in einem Workflow fungiert. Die Plattform erlaubt einfache Entwicklung neuer Aufgaben und die Integration externer Kommandozeilenprogramme. In dieser Arbeit wurde ein Plugin zur Konvertierung entwickelt, welches nutzerfreundliche Mechanismen bereitstellt, um Workflows auf verteilten Hochleistungsrechensystemen auszuführen—eine Aufgabe, die sonst technische Kenntnisse erfordert, die gewöhnlich nicht zum Anforderungsprofil eines Lebenswissenschaftlers gehören. Unsere Konverter–Erweiterung generiert quasi identische Versionen desselben Workflows, welche im Anschluss auf leistungsfähigen Berechnungsressourcen ausgeführt werden können. Infolgedessen werden nicht nur die Möglichkeiten von verteilten hochperformanten Rechensystemen sowie die Bequemlichkeit eines für Desktopcomputer entwickelte Workflowsystems ausgenutzt, sondern zusätzlich werden Berechnungsbeschränkungen von Desktopcomputern und die steile Lernkurve, die mit dem Workflowentwurf auf verteilten Systemen verbunden ist, umgangen. Unser Konverter–Plugin hat sofortige Anwendung für Forscher. Wir zeigen dies in drei für die Lebenswissenschaften relevanten Anwendungsbeispielen: Strukturelle Bioinformatik, Immuninformatik, und Metabolomik.Recent decades have witnessed an exponential increase of available biological data due to advances in key technologies for life sciences. Specialized computing resources and scripting skills are now required to deliver results in a timely fashion: desktop computers or monolithic approaches can no longer keep pace with neither the growth of available biological data nor the complexity of analysis techniques. Workflows offer an accessible way to counter against this trend by facilitating parallelization and distribution of computations. Given their structured and repeatable nature, workflows also provide a transparent process to satisfy strict reproducibility standards required by the scientific method. One of the goals of our work is to assist researchers in accessing computing resources without the need for programming or scripting skills. To this effect, we created a toolset able to integrate any command line tool into workflow systems. Out of the box, our toolset supports two widely–used workflow systems, but our modular design allows for seamless additions in order to support further workflow engines. Recognizing the importance of early and robust workflow design, we also extended a well–established, desktop–based analytics platform that contains more than two thousand tasks (each being a building block for a workflow), allows easy development of new tasks and is able to integrate external command line tools. We developed a converter plug–in that offers a user–friendly mechanism to execute workflows on distributed high–performance computing resources—an exercise that would otherwise require technical skills typically not associated with the average life scientist's profile. Our converter extension generates virtually identical versions of the same workflows, which can then be executed on more capable computing resources. That is, not only did we leverage the capacity of distributed high–performance resources and the conveniences of a workflow engine designed for personal computers but we also circumvented computing limitations of personal computers and the steep learning curve associated with creating workflows for distributed environments. Our converter extension has immediate applications for researchers and we showcase our results by means of three use cases relevant for life scientists: structural bioinformatics, immunoinformatics and metabolomics

TokenPasser: A petri net specification tool

In computer program design it is essential to know the effectiveness of different design options in improving performance, and dependability. This paper provides a description of a CAD tool for distributed hierarchical Petri nets. After a brief review of Petri nets, Petri net languages, and Petri net transducers, and descriptions of several current Petri net tools, the specifications and design of the TokenPasser tool are presented. TokenPasser is a tool to allow design of distributed hierarchical systems based on Petri nets. A case study for an intelligent robotic system is conducted, a coordination structure with one dispatcher controlling three coordinators is built to model a proposed robotic assembly system. The system is implemented using TokenPasser, and the results are analyzed to allow judgment of the tool

On the decidability of problems in liveness of controlled Discrete Event Systems modeled by Petri Nets

A Discrete Event System (DES) is a discrete-state system, where the state changes at discrete-time instants due to the occurrence of events. Informally, a liveness property stipulates that a 'good thing' happens during the evolution of a system. Some examples of liveness properties include starvation freedom -- where the 'good thing' is the process making progress; termination -- in which the good thing is for an evolution to not run forever; and guaranteed service -- such as in resource allocation systems, when every request for resource is satisfied eventually. In this thesis, we consider supervisory policies for DESs that, when they exist, enforce a liveness property by appropriately disabling a subset of preventable events at certain states in the evolution of DES. One of the main contributions of this thesis is the development of a system-theoretic framework for the analysis of Liveness Enforcing Supervisory Policies (LESPs) for DESs. We model uncertainties in the forward- and feedback-path, and present necessary and sufficient conditions for the existence of Liveness Enforcing Supervisory Policies (LESPs) for a general model of DESs in this framework. The existence of an LESP reduces to the membership of the initial state to an appropriately defined set. The membership problem is undecidable. For characterizing decidable instances of this membership problem, we consider a modeling paradigm of DESs known as Petri Nets, which have applications in modeling concurrent systems, software design, manufacturing systems, etc. Petri Net (PN) models are inherently monotonic in the sense that if a transition (which loosely represents an event of the DES) can fire from a marking (a non-negative integer-valued vector that represents the state of the DES being modeled), then it can also fire from any larger marking. The monotonicity creates a possibility of representing an infinite-state system using what can be called a "finite basis" that can lead to decidability. However, we prove that several problems of our interest are still undecidable for arbitrary PN models. That is, informally, a general PN model is still too powerful for the analysis that we are interested in. Much of the thesis is devoted to the characterization of decidable instances of the existence of LESPs for arbitrary PN models within the system-theoretic framework introduced in the thesis. The philosophical implication of the results in this thesis is the existence of what can be called a "finite basis" of an infinite state system under supervision, on which the membership tests can be performed in finite time; hence resulting in the decidability of problems and finite-time termination of algorithms. The thesis discusses various scenarios where such a finite basis exists and how to find them