For cell-biological processes, it is the complex interaction of their biochemical components, affected by both stochastic and spatial considerations, that create the overall picture. Formal modeling provides a method to overcome the limits of experimental observation in the wet-lab by moving to the abstract world of the computer. The limits of the abstract world again depend on the expressiveness of the modeling language used to formally describe the system under study. In this thesis, reaction constraints for the pi-calculus are proposed as a language for the stochastic and spatial modeling of cell-biological processes. The goal is to develop a language with sufficient expressive power to model dynamic cell structures, like fusing compartments. To this end, reaction constraints are augmented with two language constructs: priority and a global imperative store, yielding two different modeling languages, including non-deterministic and stochastic semantics. By several modeling examples, e.g. of Euglena's phototaxis, and extensive expressiveness studies, e.g. an encoding of the spatial modeling language BioAmbients, including a prove of its correctness, the usefulness of reaction constraints, priority, and a global imperative store for the modeling of cell-biological processes is shown. Thereby, besides dynamic cell structures, different modeling styles, e.g. individual-based vs. population-based modeling, and different abstraction levels, as e.g. provided by reaction kinetics following the law of Mass action or the Michaelis-Menten theory, are considered.

This work deals with the problem of visual representation of Pi-calculus expressions. The theoretical part of this paper discusses general principles of process algebras as well as specific properties of individual models, with a focus on Pi-calculus. Also included is the comparison of several text and graphical representations of expressions. The main part of the thesis deals with the design and implementation of an application for converting text representation of expressions into graphical representation. In addition to the text and graphical representation, an internal tree representation designed to work with expressions within the application is also proposed. The thesis also describes algorithms for finding feasible reductions, performing reductions and expression simplification that operate with the proposed tree representation.

Der vorliegende Band der wissenschaftlichen Schriftenreihe Eingebettete Selbstorganisierende Systeme widmet sich dem Entwurf von verteilten Eingebetteten Systemen. Einsatzgebiete solcher Systeme sind unter anderem Missions- und Steuerungssysteme von Flugzeugen (Aerospace-Anwendungen) und , mit zunehmender Vernetzung, der Automotive Bereich. Hier gilt es höchste Sicherheitsstandards einzuhalten und maximale Verfügbarkeit zu garantieren. In dieser Arbeit wird diese Problematik frühzeitig im Entwurfsprozess, in der Spezifikationsphase, aufgegriffen. Es werden Implementierungsvarianten wie Hardware und Software sowie Systemkomponenten wie Berechungskomponenten und Kommunikationskomponenten unterschieden. Für die übergreifende Spezifikation wird auf Grundlage des π-Kalküls ein formales Framework, das eine einheitliche Modellierung von Teilsystemen in den unterschiedlichen Entwurfsphasen unterstützt, entwickelt. Besonderer Schwerpunkt der Untersuchungen von Herrn Förster liegt auf Erweiterungen von Systemspezifikationen. So wird es möglich, Teilkomponenten zu verändern oder zu substituieren und die Gesamtspezifikation auf Korrektheit und Konsistenz automatisiert zu überprüfen. / This volume of the scientific series Eingebettete, selbstorganisierende Systeme (Embedded Self-Organized Systems) gives an outline of the design of distributed embedded systems. Fields of application for such systems are, amongst others, mission systems and control systems of airplanes (aeronautic applications) and - with increasing level of integration - also the automotive area. In this area it is essential to meet highest safety standards and to ensure the maximum of availability. Mr Förster addresses these problems in an early state of the design process, namely the specification. Implementation versions like hardware and software are differentiated as well as system components like computation components and communication components. For a general specification Mr Förster develops a formal framework based on the pi-calculus, which supports a standardised modelling of modules in different design steps. The main focus of Mr Förster's research is the extension of system specifications. Therefore it will be possible to modify or substitute modules and to check automatically the correctness and consistency of the total specification. Mr Förster can prove the correctness of his approach and demonstrates impressively the complexity by clearly defined extension relations and formally verifiable embedding in the pi-calculus formalism. A detailed example shows the practical relevance of this research. I am glad that Mr Förster publishes his important research in this scientific series. So I hope you will enjoy reading it and benefit from it.

Der vierte Band der wissenschaftlichen Schriftenreihe Eingebettete Selbstorganisierende Systeme widmet sich der Entwicklung von Fehlermodellen für eingebettete, verteilte Multi – Prozessorsysteme. Diese werden zu einem hierarchischen Netzwerk zur Steuerung von Flugzeugen (Avionik) verbunden und mehr und mehr im Automotive Bereich eingesetzt. Hier gilt es höchste Sicherheitsstandards einzuhalten und maximale Verfügbarkeit zu garantieren. Herr Fischer integriert die Modellierung von möglichen Fehlern in den Entwurfsprozess. Auf Grundlage des π-Kalküls entwickelt Herr Fischer ein formales Fehlermodell, das eine einheitliche Modellierung von Fehlerfällen unterstützt. Dabei werden interessante Bezüge zur Bi-Simulation sowie zu Methoden des Modell Checkings hergestellt. Die theoretischen Ergebnisse werden an einem komplexen Beispiel anschaulich illustriert. So kann der Leser die Mächtigkeit des entwickelten Ansatzes nachvollziehen und wird motiviert, die entwickelte Methodik auf weitere Anwendungsfälle zu übertragen. / The 4th volume of the scientific series Eingebettete, selbstorganisierende Systeme (Embedded Self-Organized Systems) outlines the design of fault models for embedded distributed multi processor systems. These multi processor systems will be connected to a hierarchical network to control airplanes (avionics) and also be used more and more in the automotive area. Here it is essential to meet highest safety standards and to ensure the maximum of availability. Mr Fischer integrates the modelling of potential faults into the design process. Based on the pi-calculus, he develops a formal framework, which supports a standardised modelling of faults. Thereby, interesting connections to the Bi-Simulation as well as to methods of the Model checking are established. The theoretical results are depicted on a complex example. So it is possible for the reader to understand the complexity of this approach and is motivated to use the developed methodology in other applications. I am glad that Mr Fischer publishes his important research in this scientific series.

Orientador: Mauricio Ferreira Magalhães / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Eletrica e de Computação / Made available in DSpace on 2018-08-08T01:16:08Z (GMT). No. of bitstreams: 1 Nader_MarcosVaninePortilhode_M.pdf: 1214383 bytes, checksum: 40e83a8be1c7e86e788d810a8799f6b8 (MD5) Previous issue date: 2006 / Resumo: Duas áreas importantes estão em desenvolvimento: Gerência de Processos de Negócios (Business Process Management) e Orquestração de Web Services (Web Services Orchestration). Ambas têm um objetivo que é integrar aplicações ou outros processos que tenham interfaces web services, usando o paradigma de processos de negócios. Uma linguagem que vem sendo difundida para essas aplicações é a BPEL (Business Process Execution Language). Este trabalho apresenta um framework aplicável à análise e verificação de processos de negócios escritos em BPEL através do uso de Pi-Calculus. Pi-Calculus é uma álgebra de processos que possui mecanismos formais para criação e ativação de processos que se comunicam através da troca de mensagens em canais, usando o modelo de rendezvous síncrono. Nesse framework, o processo BPEL é traduzido para um programa Pi-Calculus. Uma Máquina Virtual Pi-Calculus (MVP) recebe o programa Pi-Calculus e produz todas as reações possíveis, ou seja, gera todos os caminhos de execução que o programa pode seguir. A partir desse resultado, efetua-se a verificação de propriedades como: atendimento às especificações de mais alto nível, ordenação de eventos e ocorrência ou não de deadlocks. Em termos práticos, uma ferramenta desse tipo pode ser incorporada aos Sistemas de Gerência de Processos de Negócios (Business Process Management Systems - BPMS) para ampliar a cobertura de testes durante as fases de análise e implementação de um processo dentro do seu ciclo de vida. Nesses tipos de sistemas, a reparação de um erro durante a fase de execução é muito mais custosa que nos sistemas tradicionais / Abstract: Two important areas have been in development lately: Business Process Management and Web Service Orchestration. In both of them, the objective is to integrate applications with web services interface through business process paradigm. A number of languages have been proposed with consensus being formed around BPEL (Business Process Execution Language). This dissertation presents a framework for BPEL processes analysis and verification through Pi-Calculus. Pi-Calculus is a process algebra with formal mechanisms for processes creation and activation; these processes communicate sending and receiving messages through channels using the synchronous rendezvous model. In this framework, the BPEL process is translated to a Pi-Calculus program, A Pi-Calculus Virtual Machine (MVP) receives a Pi-calculus program and executes all possible reactions, that is, it generates all execution paths possible to be taken. With this result, the properties such as high-level specification accomplishment, events ordering and deadlock freedom are verified. In practical terms, a tool of this sort can be part of a Business Process Management System (BPMS) to broaden test coverage during the analysis and implementation phases within a process life cycle. In these kinds of systems, a repairing mistake during the execution phase is more complex than in traditional systems / Mestrado / Engenharia de Computação / Mestre em Engenharia Elétrica

Der vorliegende Band der wissenschaftlichen Schriftenreihe Eingebettete Selbstorganisierende Systeme widmet sich dem Entwurf von verteilten Eingebetteten Systemen. Einsatzgebiete solcher Systeme sind unter anderem Missions- und Steuerungssysteme von Flugzeugen (Aerospace-Anwendungen) und , mit zunehmender Vernetzung, der Automotive Bereich. Hier gilt es höchste Sicherheitsstandards einzuhalten und maximale Verfügbarkeit zu garantieren. In dieser Arbeit wird diese Problematik frühzeitig im Entwurfsprozess, in der Spezifikationsphase, aufgegriffen. Es werden Implementierungsvarianten wie Hardware und Software sowie Systemkomponenten wie Berechungskomponenten und Kommunikationskomponenten unterschieden. Für die übergreifende Spezifikation wird auf Grundlage des π-Kalküls ein formales Framework, das eine einheitliche Modellierung von Teilsystemen in den unterschiedlichen Entwurfsphasen unterstützt, entwickelt. Besonderer Schwerpunkt der Untersuchungen von Herrn Förster liegt auf Erweiterungen von Systemspezifikationen. So wird es möglich, Teilkomponenten zu verändern oder zu substituieren und die Gesamtspezifikation auf Korrektheit und Konsistenz automatisiert zu überprüfen. / This volume of the scientific series Eingebettete, selbstorganisierende Systeme (Embedded Self-Organized Systems) gives an outline of the design of distributed embedded systems. Fields of application for such systems are, amongst others, mission systems and control systems of airplanes (aeronautic applications) and - with increasing level of integration - also the automotive area. In this area it is essential to meet highest safety standards and to ensure the maximum of availability. Mr Förster addresses these problems in an early state of the design process, namely the specification. Implementation versions like hardware and software are differentiated as well as system components like computation components and communication components. For a general specification Mr Förster develops a formal framework based on the pi-calculus, which supports a standardised modelling of modules in different design steps. The main focus of Mr Förster's research is the extension of system specifications. Therefore it will be possible to modify or substitute modules and to check automatically the correctness and consistency of the total specification. Mr Förster can prove the correctness of his approach and demonstrates impressively the complexity by clearly defined extension relations and formally verifiable embedding in the pi-calculus formalism. A detailed example shows the practical relevance of this research. I am glad that Mr Förster publishes his important research in this scientific series. So I hope you will enjoy reading it and benefit from it.

Der vierte Band der wissenschaftlichen Schriftenreihe Eingebettete Selbstorganisierende Systeme widmet sich der Entwicklung von Fehlermodellen für eingebettete, verteilte Multi – Prozessorsysteme. Diese werden zu einem hierarchischen Netzwerk zur Steuerung von Flugzeugen (Avionik) verbunden und mehr und mehr im Automotive Bereich eingesetzt. Hier gilt es höchste Sicherheitsstandards einzuhalten und maximale Verfügbarkeit zu garantieren. Herr Fischer integriert die Modellierung von möglichen Fehlern in den Entwurfsprozess. Auf Grundlage des π-Kalküls entwickelt Herr Fischer ein formales Fehlermodell, das eine einheitliche Modellierung von Fehlerfällen unterstützt. Dabei werden interessante Bezüge zur Bi-Simulation sowie zu Methoden des Modell Checkings hergestellt. Die theoretischen Ergebnisse werden an einem komplexen Beispiel anschaulich illustriert. So kann der Leser die Mächtigkeit des entwickelten Ansatzes nachvollziehen und wird motiviert, die entwickelte Methodik auf weitere Anwendungsfälle zu übertragen. / The 4th volume of the scientific series Eingebettete, selbstorganisierende Systeme (Embedded Self-Organized Systems) outlines the design of fault models for embedded distributed multi processor systems. These multi processor systems will be connected to a hierarchical network to control airplanes (avionics) and also be used more and more in the automotive area. Here it is essential to meet highest safety standards and to ensure the maximum of availability. Mr Fischer integrates the modelling of potential faults into the design process. Based on the pi-calculus, he develops a formal framework, which supports a standardised modelling of faults. Thereby, interesting connections to the Bi-Simulation as well as to methods of the Model checking are established. The theoretical results are depicted on a complex example. So it is possible for the reader to understand the complexity of this approach and is motivated to use the developed methodology in other applications. I am glad that Mr Fischer publishes his important research in this scientific series.