1,671 research outputs found

    Petri nets for systems and synthetic biology

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    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

    Methodology for Integrating Computational Tree Logic Model Checking in Unified Modelling Language Artefacts A Case Study of an Embedded Controller

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    A unified modelling language (UML) based formal verification methodology that can be easily integrated into an embedded system software development life cycle is suggested. The approach augments UML diagrams with formal models through an interfacing domain and adds semantics to these diagrams. The suggested methodology; commences from functional specification and use case modelling, selects the most critical behaviour where formal verification can add value to the development cycle, analyses the selected behaviour using UML state transition diagram, derives a state chart matrix from the same, and a high level language software translates the state chart matrix to a labelled transition system. Safety properties are derived from system specifications and are expressed as computation tree logic (CTL) formulae. CTL model-checking algorithm from the literature is used for model- checking. The applicability of the suggested approach is established using a safety critical embedded controller used for deployment and recovery of sensor structures from an airborne platform

    Multi-paradigm modelling for cyber–physical systems: a descriptive framework

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    The complexity of cyber–physical systems (CPSS) is commonly addressed through complex workflows, involving models in a plethora of different formalisms, each with their own methods, techniques, and tools. Some workflow patterns, combined with particular types of formalisms and operations on models in these formalisms, are used successfully in engineering practice. To identify and reuse them, we refer to these combinations of workflow and formalism patterns as modelling paradigms. This paper proposes a unifying (Descriptive) Framework to describe these paradigms, as well as their combinations. This work is set in the context of Multi-Paradigm Modelling (MPM), which is based on the principle to model every part and aspect of a system explicitly, at the most appropriate level(s) of abstraction, using the most appropriate modelling formalism(s) and workflows. The purpose of the Descriptive Framework presented in this paper is to serve as a basis to reason about these formalisms, workflows, and their combinations. One crucial part of the framework is the ability to capture the structural essence of a paradigm through the concept of a paradigmatic structure. This is illustrated informally by means of two example paradigms commonly used in CPS: Discrete Event Dynamic Systems and Synchronous Data Flow. The presented framework also identifies the need to establish whether a paradigm candidate follows, or qualifies as, a (given) paradigm. To illustrate the ability of the framework to support combining paradigms, the paper shows examples of both workflow and formalism combinations. The presented framework is intended as a basis for characterisation and classification of paradigms, as a starting point for a rigorous formalisation of the framework (allowing formal analyses), and as a foundation for MPM tool development

    Interactive Model-Based Compilation: A Modeller-Driven Development Approach

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    There is a growing tendency for using domain-specific languages, which help domain experts to stay focussed on abstract problem solutions. It is important to carefully design these languages and tools, which fundamentally perform model-to-model transformations. The quality of both usually decides the effectiveness of the subsequent development and therefore the quality of the final applications. However, as the complexity and safety requirements of modern systems grow, it becomes increasingly burdensome to create highly customized languages and difficult to provide reasonable overviews within these tools. This thesis introduces a new interactive model-based compilation methodology. Compilations for arbitrary model-to-model transformations are themselves described as models. They can be instantiated for particular inputs, e. g. a program, to create concrete compilation runs, which return the result of that compilation. The compilation instance is interactively observable. Intermediate results serve as new inputs and as documentation. They can be used to create highly customized views and facilitate understandability. This methodology guides modellers from the start of the compilation to the final result so that they can interactively refine their models. The methodology has been implemented and validated as the KIELER Compiler (KiCo) and is available as part of the KIELER open-source project. It is used to implement the current reference compiler for the SCCharts language, a statecharts dialect designed for specifying safety-critical reactive systems based on a synchronous model of computation. The interactive model-based compilation approach was key to the rapid prototyping of three different compilation strategies, as well as new language extensions, variations and closely related languages. The results are verified with benchmarks, which are again modelled using the same approach and technology. The usability of the SCCharts language and the KiCo tooling is documented with long-term surveys and real-life industrial, academic and teaching examples

    Modeling and formal verification of probabilistic reconfigurable systems

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    In this thesis, we propose a new approach for formal modeling and verification of adaptive probabilistic systems. Dynamic reconfigurable systems are the trend of all future technological systems, such as flight control systems, vehicle electronic systems, and manufacturing systems. In order to meet user and environmental requirements, such a dynamic reconfigurable system has to actively adjust its configuration at run-time by modifying its components and connections, while changes are detected in the internal/external execution environment. On the other hand, these changes may violate the memory usage, the required energy and the concerned real-time constraints since the behavior of the system is unpredictable. It might also make the system's functions unavailable for some time and make potential harm to human life or large financial investments. Thus, updating a system with any new configuration requires that the post reconfigurable system fully satisfies the related constraints. We introduce GR-TNCES formalism for the optimal functional and temporal specification of probabilistic reconfigurable systems under resource constraints. It enables the optimal specification of a probabilistic, energetic and memory constraints of such a system. To formally verify the correctness and the safety of such a probabilistic system specification, and the non-violation of its properties, an automatic transformation from GR-TNCES models into PRISM models is introduced. Moreover, a new approach XCTL is also proposed to formally verify reconfigurable systems. It enables the formal certification of uncompleted and reconfigurable systems. A new version of the software ZIZO is also proposed to model, simulate and verify such GR-TNCES model. To prove its relevance, the latter was applied to case studies; it was used to model and simulate the behavior of an IPV4 protocol to prevent the energy and memory resources violation. It was also used to optimize energy consumption of an automotive skid conveyor.In dieser Arbeit wird ein neuer Ansatz zur formalen Modellierung und Verifikation dynamisch rekonfigurierbarer Systeme vorgestellt. Dynamische rekonfigurierbare Systeme sind in vielen aktuellen und zukünftigen Anwendungen, wie beispielsweise Flugsteuerungssystemen, Fahrzeugelektronik und Fertigungssysteme zu finden. Diese Systeme weisen ein probabilistisches, adaptives Verhalten auf. Um die Benutzer- und Umgebungsbedingungen kontinuierlich zu erfüllen, muss ein solches System seine Konfiguration zur Laufzeit aktiv anpassen, indem es seine Komponenten, Verbindungen zwischen Komponenten und seine Daten modifiziert (adaptiv), sobald Änderungen in der internen oder externen Ausführungsumgebung erkannt werden (probabilistisch). Diese Anpassungen dürfen Beschränkungen bei der Speichernutzung, der erforderlichen Energie und bestehende Echtzeitbedingungen nicht verletzen. Eine nicht geprüfte Rekonfiguration könnte dazu führen, dass die Funktionen des Systems für einige Zeit nicht verfügbar wären und potenziell menschliches Leben gefährdet würde oder großer finanzieller Schaden entstünde. Somit erfordert das Aktualisieren eines Systems mit einer neuen Konfiguration, dass das rekonfigurierte System die zugehörigen Beschränkungen vollständig einhält. Um dies zu überprüfen, wird in dieser Arbeit der GR-TNCES-Formalismus, eine Erweiterung von Petrinetzen, für die optimale funktionale und zeitliche Spezifikation probabilistischer rekonfigurierbarer Systeme unter Ressourcenbeschränkungen vorgeschlagen. Die entstehenden Modelle sollen über probabilistische model checking verifiziert werden. Dazu eignet sich die etablierte Software PRISM. Um die Verifikation zu ermöglichen wird in dieser Arbeit ein Verfahren zur Transformation von GR-TNCES-Modellen in PRISM-Modelle beschrieben. Eine neu eingeführte Logik (XCTL) erlaubt zudem die einfache Beschreibung der zu prüfenden Eigenschaften. Die genannten Schritte wurden in einer Softwareumgebung für den automatisierten Entwurf, die Simulation und die formale Verifikation (durch eine automatische Transformation nach PRISM) umgesetzt. Eine Fallstudie zeigt die Anwendung des Verfahren

    WildAniMAL - MAL Interactors Model Animator

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    Dissertação de mestrado em Engenharia de InformáticaThe IVY Workbench is a tool for modeling and analysis of interactive systems which has been developed at the Department of Informatics of the University of Minho (http://ivy.di.uminho.pt). It's a platform developed in Java, using a plugins mechanism. The available plugins include a set of editors (textual and graphical) and tools to analyse the behaviour of the models. The experience on using the tool has demonstrated the need for a model animator which could enable a first interactive evaluation of the models. Therefore this dissertation describes the design and implementation of WildAniMAL - a MAL (Modal Action Logic) interactors models animator – as a plugin for the IVY Workbench. The plugin uses the NuSMV model checker simulations capabilities, and enables users to explore the formal models interactively.A IVY Workbench é uma ferramenta de modelação e análise de sistemas interativos que tem vindo a ser desenvolvida no Departamento de Informática da Universidade do Minho (http://ivy.di.uminho.pt). Trata-se de uma plataforma desenvolvida maioritariamente em Java, utilizando um mecanismo de plugins. Os plugins existentes incluem um conjunto de editores (em modo texto e gráfico), e de ferramentas de análise do comportamento dos modelos. A experiência de utilização da ferramenta tem, no entanto, demonstrado a necessidade de um animador de modelos que permita efetuar uma primeira validação interativa dos mesmos. Sendo assim, esta dissertação descreve o desenho e implementação do WildAniMAL – um animador de modelos de MAL (Modal Action-Logic) Interactors – como plugin para a IVY Workbench. O plugin usa as capacidades de simulação do model checker NuSMV, e permite aos utilizadores explorar os modelos formais de forma interativa
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