Formal Object Interaction Language: Modeling and Verification of Sequential and Concurrent Object-Oriented Software

As software systems become larger and more complex, developers require the ability to model abstract concepts while ensuring consistency across the entire project. The internet has changed the nature of software by increasing the desire for software deployment across multiple distributed platforms. Finally, increased dependence on technology requires assurance that designed software will perform its intended function. This thesis introduces the Formal Object Interaction Language (FOIL). FOIL is a new object-oriented modeling language specifically designed to address the cumulative shortcomings of existing modeling techniques. FOIL graphically displays software structure, sequential and concurrent behavior, process, and interaction in a simple unified notation, and has an algebraic representation based on a derivative of the π-calculus. The thesis documents the technique in which FOIL software models can be mathematically verified to anticipate deadlocks, ensure consistency, and determine object state reachability. Scalability is offered through the concept of behavioral inheritance; and, FOIL’s inherent support for modeling concurrent behavior and all known workflow patterns is demonstrated. The concepts of process achievability, process complete achievability, and process determinism are introduced with an algorithm for simulating the execution of a FOIL object model using a FOIL process model. Finally, a technique for using a FOIL process model as a constraint on FOIL object system execution is offered as a method to ensure that object-oriented systems modeled in FOIL will complete their processes based activities. FOIL’s capabilities are compared and contrasted with an extensive array of current software modeling techniques. FOIL is ideally suited for data-aware, behavior based systems such as interactive or process management software

Relating state-based and process-based concurrency through linear logic (full-version)

AbstractThis paper has the purpose of reviewing some of the established relationships between logic and concurrency, and of exploring new ones.Concurrent and distributed systems are notoriously hard to get right. Therefore, following an approach that has proved highly beneficial for sequential programs, much effort has been invested in tracing the foundations of concurrency in logic. The starting points of such investigations have been various idealized languages of concurrent and distributed programming, in particular the well established state-transformation model inspired by Petri nets and multiset rewriting, and the prolific process-based models such as the π-calculus and other process algebras. In nearly all cases, the target of these investigations has been linear logic, a formal language that supports a view of formulas as consumable resources. In the first part of this paper, we review some of these interpretations of concurrent languages into linear logic and observe that, possibly modulo duality, they invariably target a small semantic fragment of linear logic that we call LVobs.In the second part of the paper, we propose a new approach to understanding concurrent and distributed programming as a manifestation of logic, which yields a language that merges those two main paradigms of concurrency. Specifically, we present a new semantics for multiset rewriting founded on an alternative view of linear logic and specifically LVobs. The resulting interpretation is extended with a majority of linear connectives into the language of ω-multisets. This interpretation drops the distinction between multiset elements and rewrite rules, and considerably enriches the expressive power of standard multiset rewriting with embedded rules, choice, replication, and more. Derivations are now primarily viewed as open objects, and are closed only to examine intermediate rewriting states. The resulting language can also be interpreted as a process algebra. For example, a simple translation maps process constructors of the asynchronous π-calculus to rewrite operators. The language of ω-multisets forms the basis for the security protocol specification language MSR 3. With relations to both multiset rewriting and process algebra, it supports specifications that are process-based, state-based, or of a mixed nature, with the potential of combining verification techniques from both worlds. Additionally, its logical underpinning makes it an ideal common ground for systematically comparing protocol specification languages

Measurements, Models, Systems and Design

531 s.

In-silico-Systemanalyse von Biopathways

Chen M. In silico systems analysis of biopathways. Bielefeld (Germany): Bielefeld University; 2004.In the past decade with the advent of high-throughput technologies, biology has migrated from a descriptive science to a predictive one. A vast amount of information on the metabolism have been produced; a number of specific genetic/metabolic databases and computational systems have been developed, which makes it possible for biologists to perform in silico analysis of metabolism. With experimental data from laboratory, biologists wish to systematically conduct their analysis with an easy-to-use computational system. One major task is to implement molecular information systems that will allow to integrate different molecular database systems, and to design analysis tools (e.g. simulators of complex metabolic reactions). Three key problems are involved: 1) Modeling and simulation of biological processes; 2) Reconstruction of metabolic pathways, leading to predictions about the integrated function of the network; and 3) Comparison of metabolism, providing an important way to reveal the functional relationship between a set of metabolic pathways. This dissertation addresses these problems of in silico systems analysis of biopathways. We developed a software system to integrate the access to different databases, and exploited the Petri net methodology to model and simulate metabolic networks in cells. It develops a computer modeling and simulation technique based on Petri net methodology; investigates metabolic networks at a system level; proposes a markup language for biological data interchange among diverse biological simulators and Petri net tools; establishes a web-based information retrieval system for metabolic pathway prediction; presents an algorithm for metabolic pathway alignment; recommends a nomenclature of cellular signal transduction; and attempts to standardize the representation of biological pathways. Hybrid Petri net methodology is exploited to model metabolic networks. Kinetic modeling strategy and Petri net modeling algorithm are applied to perform the processes of elements functioning and model analysis. The proposed methodology can be used for all other metabolic networks or the virtual cell metabolism. Moreover, perspectives of Petri net modeling and simulation of metabolic networks are outlined. A proposal for the Biology Petri Net Markup Language (BioPNML) is presented. The concepts and terminology of the interchange format, as well as its syntax (which is based on XML) are introduced. BioPNML is designed to provide a starting point for the development of a standard interchange format for Bioinformatics and Petri nets. The language makes it possible to exchange biology Petri net diagrams between all supported hardware platforms and versions. It is also designed to associate Petri net models and other known metabolic simulators. A web-based metabolic information retrieval system, PathAligner, is developed in order to predict metabolic pathways from rudimentary elements of pathways. It extracts metabolic information from biological databases via the Internet, and builds metabolic pathways with data sources of genes, sequences, enzymes, metabolites, etc. The system also provides a navigation platform to investigate metabolic related information, and transforms the output data into XML files for further modeling and simulation of the reconstructed pathway. An alignment algorithm to compare the similarity between metabolic pathways is presented. A new definition of the metabolic pathway is proposed. The pathway defined as a linear event sequence is practical for our alignment algorithm. The algorithm is based on strip scoring the similarity of 4-hierarchical EC numbers involved in the pathways. The algorithm described has been implemented and is in current use in the context of the PathAligner system. Furthermore, new methods for the classification and nomenclature of cellular signal transductions are recommended. For each type of characterized signal transduction, a unique ST number is provided. The Signal Transduction Classification Database (STCDB), based on the proposed classification and nomenclature, has been established. By merging the ST numbers with EC numbers, alignments of biopathways are possible. Finally, a detailed model of urea cycle that includes gene regulatory networks, metabolic pathways and signal transduction is demonstrated by using our approaches. A system biological interpretation of the observed behavior of the urea cycle and its related transcriptomics information is proposed to provide new insights for metabolic engineering and medical care

Semantics-driven dataflow diagram processing.

Dataflow diagram is a commonly used tool of structured analysis and design techniques in specifications and design of a software system, and in analysis of an existing system as well. While automatic generating dataflow diagram saves system designers from tedious drawing and help them develop a new system, simulating dataflow diagrams provides system analysts with a dynamic graph and help them understand an existing system. CASE tools for dataflow diagrams play an important role in software engineering. Methodologies applied to the tools are dominant issues extensively evaluated by tools designers. Executable specifications with dataflow diagrams turn out an opportunity to execute graphic dataflow diagrams for systems analysts to simulate the behavior of a system. In this thesis, a syntax representation of dataflow diagram was developed, and a formal specification for dataflow diagram was established. A parser of this developed CASE tool translates the syntax representation of DFDs into their semantic representation. An interpreter of this tool then analyzes the DFDs semantic notations and builds a set of services of a system represented by the DFDs. This CASE tool can be used to simulate system behavior, check equivalence of two systems and detect deadlock. Based on its features, this tool can be used in every phase through entire software life cycle. Paper copy at Leddy Library: Theses & Major Papers - Basement, West Bldg. / Call Number: Thesis1998 .Z46. Source: Masters Abstracts International, Volume: 39-02, page: 0535. Adviser: Indra A. Tjandra. Thesis (M.Sc.)--University of Windsor (Canada), 1998

Conceptual modelling of adaptive web services based on high-level petri nets

Service technology geared by its SOA architecture and enabling Web services is rapidly gaining in maturity and acceptance. Consequently, most worldwide (private and corporate) cross-organizations are embracing this paradigm by publishing, requesting and composing their businesses and applications in the form of (web-)services. Nevertheless, to face harsh competitiveness such service oriented cross-organizational applications are increasingly pressed to be highly composite, adaptive, knowledge-intensive and very reliable. In contrast to that, Web service standards such as WSDL, WSBPEL, WS-CDL and many others offer just static, manual, purely process-centric and ad-hoc techniques to deploy such services. The main objective of this thesis consists therefore in leveraging the development of service-driven applications towards more reliability, dynamically and adaptable knowledge-intensiveness. This thesis puts forward an innovative framework based on distributed high-level Petri nets and event-driven business rules. More precisely, we developed a new variant of high-level Petri Nets formalism called Service-based Petri nets (CSrv-Nets), that exhibits the following potential characteristics. Firstly, the framework is supported by a stepwise methodology that starts with diagrammatical UML-class diagrams and business rules and leads to dynamically adaptive services specifications. Secondly, the framework soundly integrates behavioural event-driven business rules and stateful services both at the type and instance level and with an inherent distribution. Thirdly, the framework intrinsically permits validation through guided graphical animation. Fourthly, the framework explicitly separates between orchestrations for modelling rule-intensive single services and choreography for cooperating several services through their governing interactive business rules. Fifthly, the framework is based on a two-level conceptualization: (1) the modelling of any rule-centric service with CSrv-Nets; (2) the smooth upgrading of this service modelling with an adaptability-level that allows for dynamically shifting up and down any rule-centric behavior of the running business activities

Durchführbarkeitsanalyse und Validierung eines Feldbussystems mit einer großen Anzahl an Busteilnehmern mit formalen Methoden

The complexity of large scale fieldbus systems is two-fold: message-sending concurrency and emergent bus behavior. On the one hand, an increase in the number of accumulating nodes within one fieldbus system expands its message-sending concurrency; on the other hand, the growth of emergent bus behavior causes a temporary or lasting message burst on the fieldbus channel. The message sequences in turn have an increased burst behavior, aggravating the traffic density. Therefore, this dissertation evaluates the performability of large scale fieldbus systems by presenting a busload validation procedure by formal methods. The model concept is conceptualized and formulated by UMLCD and OSI Model. Furthermore, the validation procedure is formalized and structurally specified by applying the attribute hierarchy and BMW principle. Based on sorting the message-sending occurrences from the log data of a real fieldbus-based building automation system, the validation procedure is thus quantified with the real system timed-parameters. In addition, the stochastic distributions of message transmissions are determined by the goodness of fit method. The entire work is based on DSPN as formal means of descriptions and models. The corresponding Petri net communication model is hierarchically constructed, which has been further parameterized, integrated and simulated. The analysis of system complexity is provided by the programming-based extension of the Petri net communication model. In addition, the results of Monte-Carlo-Simulation have been sorted, analyzed and evaluated regarding the validation aspects of system performability. Finally, the emergent message burst generated from the function interrelations has also been observed and evaluated. The result of this work will make a formal contribution to the improvement the fieldbus specification.Insbesondere für Feldbussysteme mit einer großen Anzahl an Busteilnehmern wird die Komplexität über zwei Kenngrößen charakterisiert. Einerseits stellt die Erhöhung der Anzahl akkumulierter Feldbusknoten innerhalb eines Feldbussystems eine gestiegene Message-Sendung-Nebenläufigkeit dar. Andererseits steigt diese auch durch Zuwachs des emergenten Busverhaltens, die temporäre oder dauerhafte Nachrichtenfolgen mit sich führen. Die Nachrichtenfolgen wiederum können ein erhöhtes Burst-Verhalten auf dem Feldbus-Kanal, d.h. eine erhöhte Busauslastung verursachen. Ziel der vorliegenden Arbeit ist es, ein komplexes Feldbussystem formal zu beschreiben und ein formales Buslastvalidierungsverfahren darzustellen. Das Modellkonzept wird zunächst durch das UMLCD und das OSI-Modell formuliert, und anschließend wird das Validierungsverfahren mit der Attributhierarchie und dem BMW-Prinzip formalisiert und spezifiziert. Aufgrund der Sortierung des Sendungsverhaltens mittels Logdaten eines realen Feldbus-basierten Gebäudeautomationssystems, wird das Validierungsverfahren durch die quantitative Analyse weitergeführt. Zusätzlich werden die stochastischen Verteilungen der Sendungsverhaltene durch die Goodness-of-Fit Methode angepasst. Die gesamte Arbeit basiert auf DSPN als formales Beschreibungsmittel und Modellierungsmittel. Das entsprechende Petrinetz-Kommunikationsmodell wird vorgestellt, welches hierarchisch konstruiert, parametriert und simuliert wurde. Die Systemkomplexität wird mit Hilfe der Programmierung-basierten Erweiterung des Petrinetz-Kommunikationsmodells analysiert. Dazu werden die Monte-Carlo-Simulationsergebnisse dieses erweiterten Modells vorgestellt, analysiert und bewertet und in Bezug zu den Validierungsaspekten der Systemleistung gesetzt. Schließlich wird das erzeugte Nachrichten-Burst-Verhalten von den Funktionsverknüpfungen beobachtet und bewertet. Die Ergebnisse werden von dieser Arbeit nach der Vervollständigung der formalen Feldbusspezifikation zurückgeführt und verbessert