The purpose of this MSc thesis is to create design and implementation of program for translation of x86 binary code to a high-level programming language. There is described PE file format for executables used in MS Windows operating systems in the first part of work. This document contains general information about instruction set IA-32, especially a way of decoding binary code to assembly language. There are described typical program constructions, which are being used in compilers. Design of creation high-level programming language was inspired by existing programming languages. Conclusion is made about advantages and disadvantages of approach used in this thesis.

<p dir="ltr">This thesis focuses on securing different attack surfaces of embedded systems while meeting the stringent requirements imposed by these systems. Due to the specialized architecture of embedded systems, the security measures should be customized to match the unique requirements of each specific domain. To this end, this thesis identified novel security architectures using techniques such as anomaly detection, program analysis, compartmentalization, etc. This thesis synergizes work at the intersection of programming languages, compilers, computer architecture, operating systems, and embedded systems. </p>

The Golog action programming language is a powerful means to express high-level behaviours in terms of programs over actions defined in a Situation Calculus theory. In particular for physical systems, verifying that the program satisfies certain desired temporal properties is often crucial, but undecidable in general, the latter being due to the language’s high expressiveness in terms of first-order quantification and program constructs. So far, approaches to achieve decidability involved restrictions where action effects either had to be contextfree (i.e. not depend on the current state), local (i.e. only affect objects mentioned in the action’s parameters), or at least bounded (i.e. only affect a finite number of objects). In this paper, we present a new, more general class of action theories (called acyclic) that allows for context-sensitive, non-local, unbounded effects, i.e. actions that may affect an unbounded number of possibly unnamed objects in a state-dependent fashion. We contribute to the further exploration of the boundary between decidability and undecidability for Golog, showing that for acyclic theories in the two-variable fragment of first-order logic, verification of CTL properties of programs over ground actions is decidable.

In der Bioinformatik und der Next-Generation Sequenzierung benötigen wir oft große und komplexe Verarbeitungsabläufe um Daten zu analysieren. Die Werkzeuge und Bibliotheken, die hierin die Verarbeitungsschritte bilden, stammen aus unterschiedlichen Quellen und exponieren unterschiedliche Schnittstellen, was ihre Integration in Datenanalyseplattformen erschwert. Hinzu kommt, dass diese Verarbeitungsabläufe meist große Datenmengen prozessieren weshalb Forscher erwarten, dass unabhängige Verarbeitungsschritte parallel laufen. Der Stand der Technik im Feld der wissenschaftlichen Datenverarbeitung für Bioinformatik und Next-Generation Sequenzierung sind wissenschaftliche Workflowsysteme. Ein wissenschaftliches Workflowsystem erlaubt es Forschern Verarbeitungsabläufe als Workflow auszudrücken. Solch ein Workflow erfasst die Datenabhängigkeiten in einem Verarbeitungsablauf, integriert externe Software und erlaubt es unabhängige Verarbeitungsschritte zu erkennen, um sie parallel auszuführen. In dieser Arbeit präsentieren wir Cuneiform, eine Workflowsprache, und ihre verteilte Ausführungsumgebung. Für Cuneiform's Design nehmen wir die Perspektive der Programmiersprachentheorie ein. Wir lassen Methoden der funktionalen Programmierung einfließen um Komposition und Datenabhängigkeiten auszudrücken. Wir nutzen operationelle Semantiken um zu definieren, wann ein Workflow wohlgeformt und konsistent ist und um Reduktion zu erklären. Für das Design der verteilten Ausführungsumgebung nehmen wir die Perspektive der verteilten Systeme ein. Wir nutzen Petri Netze um die Kommunikationsstruktur der im System beteiligten Agenten zu erklären. / Bioinformatics and next-generation sequencing data analyses often form large and complex pipelines. The tools and libraries making up the processing steps in these pipelines come from different sources and have different interfaces which hampers integrating them into data analysis frameworks. Also, these pipelines process large data sets. Thus, users need to parallelize independent processing steps. The state of the art in large-scale scientific data analysis for bioinformatics and next-generation sequencing are scientific workflow systems. A scientific workflow system allows researchers to describe a data analysis pipeline as a scientific workflow which integrates external software, defines the data dependencies forming a data analysis pipeline, and parallelizes independent processing steps. Scientific workflow systems consist of a workflow language providing a user interface, and an execution environment. The workflow language determines how users express workflows, reuse and compose workflow fragments, integrate external software, how the scientific workflow system identifies independent processing steps, and how we derive optimizations from a workflow's structure. The execution environment schedules and runs data processing operations. In this thesis we present Cuneiform, a workflow language, and its distributed execution environment. For Cuneiform's design we take the perspective of programming languages. We adopt methods from functional programming towards composition and expressing data dependencies. We apply operational semantics and type systems to define well-formedness, consistency, and reduction of Cuneiform workflows. For the design of the distributed execution environment we take the perspective of distributed systems. We apply Petri nets to define the communication patterns among the distributed execution environment's agents.

Simulationssprachen sind in Bezug auf die Unterstützung neuer domänenspezifischer Konzepte mit einer dem Problem entsprechenden prägnanten Darstellung nicht flexibel erweiterbar. Dies betrifft sowohl die Sprache in ihren Konzepten als auch die Unterstützung der Sprache durch Sprachwerkzeuge. In dieser Arbeit entsteht der neue Sprachentwicklungsansatz Discrete-Event Modelling with Extensibility (DMX) für die Entwicklung flexibel erweiterbarer Simulationssprachen für domänenspezifische Anwendungsfelder, der eine effiziente Entwicklung der Sprache und eine effiziente Ausführung von Modellen erlaubt. Der Fokus der Arbeit liegt auf der zeitdiskreten ereignisbasierten Simulation und einer prozessorientierten Beschreibung von Simulationsmodellen. Der Ansatz unterscheidet Basiskonzepte, die zur Basissprache gehören, und Erweiterungskonzepte, die Teil von Erweiterungsdefinitionen sind. Es wird untersucht, welche Basiskonzepte eine Simulationssprache bereitstellen muss, so dass eine laufzeiteffiziente Ausführung von prozessorientierten Modellen möglich ist. Die hohe Laufzeiteffizienz der Ausführung wird durch die Konzeption einer neuartigen Methode zur Abbildung von Prozesskontextwechseln auf ein C++-Programm gezeigt. Der Spracherweiterungsansatz ist nicht auf Simulationssprachen als Basissprachen beschränkt und wird daher allgemein beschrieben. Der Ansatz basiert auf einer Syntaxerweiterung einer Basissprache, die mit einem Metamodell und einer kontextfreien Grammatik definiert ist. Die Ausführung von Erweiterungskonzepten wird durch eine Konzeptreduktion auf Basiskonzepte erreicht. Der Ansatz stellt bestimmte Voraussetzungen an eine Basissprache und erlaubt bestimmte Arten von Erweiterungen, die in der Arbeit untersucht werden. Die Eignung des Anstatzes zur Entwicklung einer komplexen domänenspezifischen Simulationssprache wird an einer Sprache für Zustandsautomaten gezeigt. / Simulation languages are not extensible regarding the support of new domain-specific concepts with a concise representation. This includes the concepts of a language as well as the language tools. In this dissertation, the new approach Discrete-Event Modelling with Extensibility (DMX) is developed. DMX allows to create flexible domain-specific simulation languages by defining extensions to a base language. The approach allows to develop these languages efficiently and also to execute simulation models in a runtime efficient way. The focus of this dissertation is on process-oriented descriptions of discrete-event simulation models. The approach distinguishes base concepts which are part of the base language and extension concepts which are part of extension definitions. The dissertation investigates the necessary base concepts which should be included in a base simulation language in order to execute process-oriented models efficiently. The high runtime efficiency of executions is achieved by creating a new method for mapping process context switches to a program in C++. The runtime efficiency can be transferred to extension concepts as well. The extension approach is described in a general way because it is not limited to a simulation language as a base language. The approach is based on the syntax extension of a base language, which is defined by a metamodel and a context-free grammar. The execution of extension concepts is achieved by concept reduction to base concepts. The approach has a number of requirements to the base language and allows certain kinds of extensions, which are desribed in the dissertation. The possibility to define a complex domain-specific simulation language is shown by applying the approach to the development of a state machine language.

[pt] Com a evolução da Internet e o crescente sucesso de ambientes Web como plataformas genéricas de aplicação, expandiram-se as necessidades de integração e coordenação de componentes de software heterogêneos e autônomos. Os requisitos específicos deste contexto impulsionaram uma nova leva de trabalhos sobre mecanismos de coordenação, dentre os quais o espaço de tuplas reativo. Neste trabalho apresentamos LuaTS, um espaço de tuplas reativo com uma dinâmica de execução orientada a eventos e com suporte apenas a chamadas assíncronas. Desenvolvido em Lua, o sistema incorpora funcionalidades diferenciadas que permitem ao programador expandir a sua semântica básica e flexibilizam o processo de busca e recuperação de tuplas. Descrevemos a implementação de LuaTS e exploramos suas particularidades através de alguns exemplos, incluindo problemas clássicos de programação concorrente e distribuída. Conforme ilustramos, os benefícios do desacoplamento proporcionado pelo modelo de espaço de tuplas, aliados à dinâmica de programação orientada a eventos, simplificam a sincronização inter-processos e geram um fluxo de execução mais claro, reduzindo em muitos casos o esforço associado ao desenvolvimento de aplicações distribuídas. / [en] The widespread use of the Internet along with the rapid growth and acceptance of the Web as a general application platform impose new requirements associated with the integration and coordination of autonomous and heterogeneous software components. The specific needs of this context led to the development of new coordination mechanisms, among which the reactive tuple space. In this work we present LuaTS, a reactive, event oriented tuple space that supports only asynchronous calls. The system, developed in Lua, provides functionalities that allow programmers to extend its basic semantics and also support a more flexible tuple search and retrieval process. We describe the implementation of LuaTS and explore its features through different examples that include classic concurrent and distributed programming problems. We show that the uncoupling provided by the tuple space model, together with an event oriented programming dynamics,simplify inter- process synchronization and yield a clear execution stream, improving, in many cases, the development process of distributed applications.

The Generalized Finite Element Method (GFEM) is a numerical method based on the Partition of Unity (PU) concept and inspired on both the Partition of Unity Method (PUM) and the hp-Cloud method. According to the GFEM, the PU is provided by first-degree Lagragian interpolation functions, defined over a mesh of elements similar to the Finite Element Method (FEM) meshes. In fact, the GFEM can be considered an extension of the FEM to which enrichment functions can be applied in specific regions of the problem domain to improve the solution. This technique has been successfully employed to solve problems presenting discontinuities and singularities, like those that arise in Fracture Mechanics. However, most publications on the method are related to linear analyses. The present thesis is a contribution to the few studies of nonlinear analyses of Solid Mechanics by means of the GFEM. One of its main topics is the derivation of a segment-to-segment generalized contact element based on the mortar method. Material and kinematic nonlinear phenomena are also considered in the numerical models. An Object-Oriented design was developed for the implementation of a GFEM nonlinear analyses framework written in Python programming language. The results validated the formulation and demonstrate the gains and possible drawbacks observed for the GFEM nonlinear approach. / O Método dos Elementos Finitos Generalizados (MEFG) é um método numérico baseado no conceito de partição da unidade (PU) e inspirado no Método da Partição da Unidade (MPU) e o método das Nuvens-hp. De acordo com o MEFG, a PU é obtida por meio de funções de interpolação Lagragianas de primeiro grau, definidas sobre uma rede de elementos similar àquela do Método dos Elementos Finitos (MEF). De fato, o MEFG pode ser considerado uma extensão do MEF para a qual se pode aplicar enriquecimentos em regiões específicas do domínio, buscando melhorias na solução. Esta técnica já foi aplicada com sucesso em problemas com descontinuidades e singularidades, como os originários da Mecânica da Fratura. Apesar disso, a maioria das publicações sobre o método está relacionada a análises lineares. A presente tese é uma contribuição aos poucos estudos relacionados a análises não-lineares de Mecânica dos Sólidos por meio do MEFG. Um de seus principais tópicos é o desenvolvimento de um elemento de contato generalizado do tipo segmento a segmento baseado no método mortar. Fenômenos não lineares devidos ao material e à cinemática também são considerados nos modelos numéricos. Um projeto de orientação a objetos para a implementação de uma plataforma de análises não-lineares foi desenvolvido, escrito em linguagem de programação Python. Os resultados validam a formulação e demonstram os ganhos e possíveis desvantagens da abordagem a problemas não lineares por meio do MEFG.

Les travaux réalisés dans le cadre de cette thèse ont pour objectif de proposer un langage de description temporelle pour des systèmes temps-réel et d’établir les conditions de leur ordonnançabilité sous l’algorithme Earliest Deadline First (EDF). Les langages de description temporelle permettent de spécifier le comportement temporel d’une application indépendamment de son comportement fonctionnel. Le programmeur déclare dans ces langages à quels instants précis doivent être déclenchées et terminées les activités du système. Cette gestion du temps, précise et explicite, apporte au système son caractère déterministe. Le langage proposé, Extended Timing Definition Language (E-TDL), étend des langages dirigés par le temps existants, en particulier Giotto et TDL, en introduisant un nouveau modèle de tâche donné par quatre paramètres : phase, pire temps d’exécution, temps d’exécution logique TEL (intervalle de temps séparant le lancement de la tâche et sa terminaison) et période. L’introduction de ce nouveau modèle de tâche nécessite de revisiter en particulier le problème de l’ordonnançabilité des tâches pour EDF. Cette thèse propose et développe une analyse basée sur la fonction de demande pour des ensembles de tâches décrites en E-TDL et s’exécutant en contexte monoprocesseur. Une condition nécessaire et suffisante est obtenue au travers d’une analyse précise des intervalles séparant les activations de tâches au sein de différents modules s’exécutant indépendamment et pouvant changer de mode à des instants prédéfinis. Une borne de la longueur des intervalles sur lesquels doit s’opérer la vérification est déterminée. Un outil mettant en œuvre cette analyse a été développé. / The goal of this research is to define a time-triggered language for modeling real-time systems and to provide the conditions for their schedulability under Earliest Deadline First (EDF). Time-triggered languages separate the functional part of applications from their timing definition. These languages permit to model the real-time system temporal behavior by assigning system activities to particular time instants. We propose a new time-triggered framework, Extended Timing Definition Language (E-TDL), that enhances the basic task model used in Giotto and TDL while keeping compositional and modular structure brought by the latter. An E-TDL task is characterized by: an offset, a worst case execution time, a Logical Execution Time (a time interval between task release and its termination) and a period. The schedulability analysis of the system based on this new task model should be, in particular for EDF, investigated. We develop, on the concept of the processor demand criterion, conditions for the feasibility of an E-TDL system running on a single CPU under EDF. A necessary and sufficient condition is obtained by considering the global schedules that are made up of execution traces occurring at the same time in distinct modules that are able to switch their modes at predefined instants. We estimate a maximal length of the interval on which the schedulability condition must be checked. A tool suite performing the schedulability analysis of the E-TDL systems is developed.

O mapeamento e a estimação de riscos e incidências são ferramentas muito úteis para a Epidemiologia pois, auxiliam na prevenção de agravos da saúde e, também auxiliam no planejamento e avaliação dos serviços de saúde. Este trabalho busca utilizar uma ferramenta estatística que incorpora de forma adequada este tipo de análise ao estudo de outras características que estejam relacionadas a estes agravos. No presente trabalho utiliza-se como aplicação dados do estudo caso-controle espacial com base populacional de acidentes de trabalho com a proposta de estimar a distribuição espacial do risco de sofrer acidente de trabalho na área urbana do município de Piracicaba/SP entre trabalhadores que se encontravam na situação de precarização do trabalho em associação com outras variáveis de interesse através de modelos aditivos generalizados (MAG) e, através disso, mostrar que ao incorporar de forma explícita o espaço no processo de modelagem dos dados ocorre um ganho significativo na explicação da variação do risco. O modelo MAG utilizado tem variável resposta binomial (caso e controle) e multinomial (caso e controle separados pela gravidade do acidente sofrido). Com os modelos ajustados, mapas foram desenhados com indicações de diferentes cores para a intensidade do risco de sofrer acidente de trabalho. Outra abordagem utilizada para os dados espaciais de acidentes de trabalho foi a INLA (INTEGRATED NESTED LAPLACE APPROXIMATIONS), a qual é utilizada como processo de modelagem para a família dos modelos Gaussianos latentes através de novos métodos para esta família de modelos. A intenção foi mostrar como essa nova abordagem lida com dados do tipo espacial e, fazer uma comparação com a abordagem feita pela modelagem GAM / Mapping and estimation of risks and impacts are very useful tools for Epidemiology at the assistance in prevention of injuries and health, also assists in planning and evaluation of health services. This paper seeks to use a statistical tool that adequately incorporates this type of analysis to the study of other characteristics that are related these illnesses. In the present work is used as application data from case-control study space-based population accidents with the proposal to estimate the spatial distribution of risk of suffering an accident at work in the urban area of Piracicaba/SP among workers who were in employed as casual labor in combination with other variables of interest using generalized additive models (GAM) and, thereby, show that by incorporating explicitly space in the process of data modeling is a gain significant in explaining the variation in risk. The GAM model have used binomial response variable (case and control) and multinomial (case and control separated by the severity of the accident suffered). With the adjusted models, maps were drawn with indications of different colors to the intensity of the risk of accident. Another approach used for spatial data on accidents at work was the INLA (INTEGRATED NESTED LAPLACE APPROXIMATIONS), which is used as a modeling process for the family of latent Gaussian models through new methods for this family of models. The intention was to show how this new approach deals with spatial data and a comparison with the approach made by GAM modeling.

O mapeamento e a estimação de riscos e incidências são ferramentas muito úteis para a Epidemiologia pois, auxiliam na prevenção de agravos da saúde e, também auxiliam no planejamento e avaliação dos serviços de saúde. Este trabalho busca utilizar uma ferramenta estatística que incorpora de forma adequada este tipo de análise ao estudo de outras características que estejam relacionadas a estes agravos. No presente trabalho utiliza-se como aplicação dados do estudo caso-controle espacial com base populacional de acidentes de trabalho com a proposta de estimar a distribuição espacial do risco de sofrer acidente de trabalho na área urbana do município de Piracicaba/SP entre trabalhadores que se encontravam na situação de precarização do trabalho em associação com outras variáveis de interesse através de modelos aditivos generalizados (MAG) e, através disso, mostrar que ao incorporar de forma explícita o espaço no processo de modelagem dos dados ocorre um ganho significativo na explicação da variação do risco. O modelo MAG utilizado tem variável resposta binomial (caso e controle) e multinomial (caso e controle separados pela gravidade do acidente sofrido). Com os modelos ajustados, mapas foram desenhados com indicações de diferentes cores para a intensidade do risco de sofrer acidente de trabalho. Outra abordagem utilizada para os dados espaciais de acidentes de trabalho foi a INLA (INTEGRATED NESTED LAPLACE APPROXIMATIONS), a qual é utilizada como processo de modelagem para a família dos modelos Gaussianos latentes através de novos métodos para esta família de modelos. A intenção foi mostrar como essa nova abordagem lida com dados do tipo espacial e, fazer uma comparação com a abordagem feita pela modelagem GAM / Mapping and estimation of risks and impacts are very useful tools for Epidemiology at the assistance in prevention of injuries and health, also assists in planning and evaluation of health services. This paper seeks to use a statistical tool that adequately incorporates this type of analysis to the study of other characteristics that are related these illnesses. In the present work is used as application data from case-control study space-based population accidents with the proposal to estimate the spatial distribution of risk of suffering an accident at work in the urban area of Piracicaba/SP among workers who were in employed as casual labor in combination with other variables of interest using generalized additive models (GAM) and, thereby, show that by incorporating explicitly space in the process of data modeling is a gain significant in explaining the variation in risk. The GAM model have used binomial response variable (case and control) and multinomial (case and control separated by the severity of the accident suffered). With the adjusted models, maps were drawn with indications of different colors to the intensity of the risk of accident. Another approach used for spatial data on accidents at work was the INLA (INTEGRATED NESTED LAPLACE APPROXIMATIONS), which is used as a modeling process for the family of latent Gaussian models through new methods for this family of models. The intention was to show how this new approach deals with spatial data and a comparison with the approach made by GAM modeling.