Cybersecurity classes focus on building practical skills alongside the development of the open mindset that is essential to tackle the dynamic cybersecurity landscape. Unfortunately, traditional lecture-style teaching is insufficient for this task. Peer instruction is a non-traditional, active learning approach that has proven to be effective in computer science courses. The challenge in adopting peer instruction is the development of conceptual questions. This thesis presents a methodology for developing peer instruction questions for cybersecurity courses, consisting of four stages: concept identification, concept trigger, question presentation, and development. The thesis analyzes 279 questions developed over two years for three cybersecurity courses: introduction to computer security, network penetration testing, and introduction to computer forensics. Additionally, it discusses examples of peer instruction questions in terms of the methodology. Finally, it summarizes the usage of a workshop for testing a selection of peer instruction questions as well as gathering data outside of normal courses.

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Visualization of digital geographic data is often accomplished through custom symbology that is saved in a proprietary format called a layer file (.lyr). The sharing of free geographical information system (GIS) data can be limited as the symbology data is bound inthe .lyr file format. This makes it harder and more tedious to work with open software tools since it is not possible to convert or open the .lyr file in free and open GIS software and thus limits the distribution of free GIS data. The aim of this thesis is to increase the interoperability of .lyr data between proprietary and free and open GIS software. This was done by revers eengineering the .lyr file format to document the file structure and to distribute the knowledge and metadata gained from this project to the open source community. Reverse engineering the.lyr format provided a well needed metadata and documentation about the format which increases the interoperability and enable future work to continue to lessen the gap between open source and commercial software. This groundwork can therefore, enable a continued development of data interoperability between proprietary and free and open GIS software.

Targeting of key events in viral infection pathways creates opportunities for virus disease prevention and therapy. Nanoparticles with well-defined surfaces are promising tools for the direct visualization of biological processes and for interrogating virus behavior that is usually determined by the synergistic interplay of multiple factors and involves various transient signaling steps. Smart nanoparticles mimicking enveloped viral particles are thus developed and tested in this work with the aim to de-couple key steps in human immune-deficiency virus HIV-1 trans-infection with an engineerable viral model system. Uni-lamellar liposomes resemble biological lipid bilayer membrane structures with tunable particle size, surface charge, and composition. Pretreatment with ganglioside-GM3-containing liposomes inhibited the binding of HIV-1 by dendritic cells, indicating an essential role for GM3 in virus binding. To equip the liposome based model systems with strong non bleaching optical properties, the membranes were in the next step assembled around noble metal nanoparticle core. Noble metal nanoparticles with a size of 20nm-100nm have extraordinarily large scattering cross-sections and enable prolonged tracking of even individual particles with high temporal and spatial resolutions. The plasmon resonance peak of near-field coupled gold nanoparticles red-shifts within decreasing interparticle separation. The distance dependent optical properties of noble metal nanoparticles were utilized for characterizing clustering levels of breast cancer cell marker protein CD24 and CD44 on immortalized cancer cell lines. These encouraging results supported the choice of gold nanoparticles as core for multi-modal artificial virus nanoparticles. Artificial virus nanoparticles combine the biological versatility of a self-assembled membrane with the unique optical properties of a nanoparticle core. We developed these hybrid materials specifically for the purpose of elucidating key steps of the glycoprotein independent binding and uptake of HIV-1 during trans-infection. Systematic validation experiments revealed that GM3 containing artificial virus nanoparticles (AVNs) recapitulate the initial capture and uptake of viruses by sialoadhesin CD169 presenting cells. The AVNs also reproduced the tendency of the virus to re-distribute into confined cluster spots in cell peripheral areas. Upon contact formation between T cell and DC, the AVNs developed a polarized distribution in which they enriched at the interface between DC and CD4+ T cells. The multimodality of the AVNs was instrumental in determining the detailed location and kinetics of the nanoparticles during the trans-infection process, proving the AVN system to be a unique model system to address key mechanistic questions in the infection pathway of enveloped virus particles.

A execução da engenharia reversa orientada a objetos de um sistema legado desenvolvido com orientação procedimental é usada como base para sua reengenharia, seguindo duas abordagens diferentes. Na primeira, o sistema passa por reengenharia com mudança de orientação, por meio de segmentação e, posteriormente, é transformado para uma linguagem orientada a objetos de forma semi-automática. Na segunda, é feito o reconhecimento de padrões recorrentes de software no modelo de objetos produzido pela engenharia reversa, para depois efetuar a reengenharia utilizando esses padrões. Os resultados obtidos por intermédio dessas duas abordagens podem ser comparados quanto à manutenibilidade, legibilidade e reuso. A versão original do sistema legado escolhido para a realização da experiência está implementado na linguagem Clipper e possui cerca de vinte mil linhas de código. Trata-se de uma oficina auto-elétrica e mecânica de veículos. Para a engenharia reversa foi escolhido o método Fusion/RE, sendo feita uma proposta para sua evolução, adicionando um maior detalhamento da etapa de abstração do modelo de análise do sistema. Para mudança de orientação do paradigma de desenvolviemnto, de procedimental para orientado a objetos, são propostas duas etapas adicionais a serem executadas após a aplicação do Fusion/RE: o projeto avante do sistema e a segmentação do programa legado. Indicações sobre como fazer a segmentação são fornecidas. A transformação do código segmentado em Clipper para Java é feita com auxílio da máquina Draco-Puc. Uma estratégia é proposta para o reconhecimento de padrões a partir do modelo de objetos do sistema obtido pela engenharia reversa. Por meio dela, instâncias dos padrões Type-Object, Association-Object, State Across a Collection e Behaviour Across a Collection podem ser reconhecidas. Experiências de implementação de alguns desses padrões, em Delphi, são feitas. / The object oriented reverse engineering of a legacy system, originally developed using the procedural paradigm, is the basis for two different reengineering approaches. In the first, the reengineering is done to change the implementation paradigm by segmentation, followed by the semi-automatic transformation to an object oriented language. In the second, recurring patterns are first recognized in the object model produced by the reverse engineering, and then the reengineering is done adopting these patterns. Results obtained by these two approaches are compared to assess their maintainability, legibility and reuse. The original version of the legacy system used in this experience has about twenty thousand lines of Clipper code and refers to an electric and mechanic car repair shop. For the reverse engineering phase the Fusion/RE method is used, and a proposal is done for its evolution, adding features to detail its system analysis model abstraction phase. To change the system orientation paradigm, from procedural to object-oriented, two additional phases are proposed to be conducted after the application of the Fusion/RE method: the forward design of the system and the legacy code segmentation. Hints and rationales are supplied to conduct the code segmentaion. The code transformation from segmented Clipper to Java is done with support of the Draco-Puc machine. A strategy is proposed for pattern recognition based on the system object model obtained through reverse engineering. Through it, instances of Type-Object, Association-Object, State Across a Collection and Behaviour Across a Collection patterns can be recognized. Delphi implementation experiments of these patterns are done.

La rétro-ingénierie consiste à reconstruire un modèle paramétrique à partir d'un nuage de points ou d'un maillage 3D représentant un objet, afin d'en déterminer le processus de conception ou de fabrication. Ce modèle correspond à une combinaison de primitives géométriques (cylindres, plans, sphères...) dont on cherche à estimer les paramètres à partir des données 3D. La rétro-ingénierie est très utilisée dans l'industrie de pièces manufacturées pour l'analyse métrologique, le contrôle non destructif ou la compréhension d'un procédé de fabrication.Cette thèse, menée en collaboration avec la société C4W, s'intéresse à l'extraction de primitives géométriques à partir d'un maillage 3D issu de la numérisation d'un objet manufacturé. La particularité de ces maillages est qu'ils contiennent de nombreuses imprécisions par rapport au plan CAO initial, engendrées à la fois par la fabrication de l'objet et par sa numérisation.Nous nous sommes d'abord intéressés à l'amélioration des techniques existantes afin d'extraire des primitives robustes aux imprécisions des données. Nous avons en particulier exploré plusieurs approches telles que la segmentation préalable du maillage, la caractérisation de la forme à l'aide des courbures et l'approximation d'une primitive par régression ou optimisation sur les points du maillage.Le second axe de cette thèse consiste à embellir le modèle paramétrique reconstruit, c'est-à-dire à régulariser les paramètres des primitives afin qu'elles respectent des relations géométriques telles que le parallélisme ou la concentricité. Nous nous sommes donc intéressés à différents aspects de la conception CAO induisant ces relations. Ainsi, nous cherchons à détecter automatiquement des éléments de références (repère, plans ou droites d'appuis) ayant permis de modéliser la pièce originale. Ces derniers servent alors de références absolues pour un embellissement global des primitives.Le troisième axe de recherche concerne la reconnaissance de motifs particuliers à partir de l'ensemble des primitives. Nous nous sommes ainsi intéressés aux entités d'usinage et aux répétitions de géométrie, fréquemment construites lors de la conception d'une pièce manufacturée. Cette seconde analyse de l'objet, plus fonctionnelle, permet de déduire de nouvelles informations liées à la fabrication d'une pièce. / A reverse engineering process allows to reconstruct a parametric model from a 3D point cloud or a 3D mesh of an object. The main objective is to retrieve information about the original modeling or fabrication process. The reconstructed model corresponds to a combination of geometric primitives (cylinders, planes, spheres...). These primitives are defined by parameters which are estimated from the 3D input data. Reverse engineering is mainly used in industry, for example in metrology analysis, non-destructive inspection or functional analysis.This thesis, in collaboration with the C4W company, concerns the extraction of geometric primitives from a digitized 3D mesh which represents a manufactured part. This type of mesh often contains many inaccuracies unlike the original CAD model. These inaccuracies can come from both fabrication and digitization processes.First, we try to improve existing techniques to extract robust primitives. Thus, we explore some approaches such as mesh segmentation, shape caracterization based on discrete curvatures and primitive fitting using regression and optimization techniques.The second research axis of this thesis concerns a process called "beautification", which tries to regularize the primitive parameters with respect to geometric relations such as parallelism or concentricity. To do that, we propose an analysis of the primitives, related to standard CAD modeling rules. So, we automatically detect reference elements (coordinate system, planes or lines). In order to guide the model reconstruction, we use these references to regularize the primitives globally.The third research axis concerns the pattern recognition from a set of primitives. So, we search for mechanical features (counterbore, pocket...) and repetitions (linear, circular...), which are often used in CAD modeling of manufactured part. This second analysis, more functionnal, allows to deduce more information related to the modeling and fabrication processes.

Modelamento médico é uma técnica utilizada por cirurgiões no auxílio da diagnose, comunicação com o paciente, estudos pré-operatórios, definição e simulação de procedimentos cirúrgicos, visando diminuir o tempo cirúrgico e de convalescença do paciente. Em aplicações mais recentes, esta técnica tem sido utilizada no desenvolvimento de próteses personalizadas, possibilitando que reconstituições de grande complexidade sejam feitas de maneira rápida e segura. Resumidamente, a técnica consiste em produzir um protótipo em terceira dimensão do tecido ou deformidade em estudo. Utiliza-se hoje de modernas tecnologias como tomografia computadorizada e prototipagem rápida entre outras, representando um exemplo significativo de integração entre diferentes áreas do conhecimento. Este trabalho apresenta e discute o modelamento médico no que se refere às suas aplicações, enfocando a integração entre as tecnologias de prototipagem rápida, engenharia reversa (RE) e projeto e engenharia assistidos por computador (CAD/CAE). É feita uma descrição dos procedimentos de geração dos modelos médicos usando técnicas de prototipagem rápida a partir de dados obtidos de tomografia computadorizada, e um estudo de sua precisão dimensional e geométrica. São explorados os recursos possibilitados pela integração com sistemas CAD/CAE, e apresentadas aplicações reais das técnicas na área de cirurgias craniofaciais, evidenciando as vantagens de sua utilização e validando os procedimentos propostos. / Medical modeling is a technique used by surgeons in the diagnosis, communication with the patient, preoperative studies, definition and simulation of surgical procedures. It helps to reduce the operative and convalescence time. It consists of producing a prototype in third dimension of the tissue or deformity in study. In some more recent applications, this technique has been used to develop customized prosthesis, enabling that quite complex reconstructions can be made in a safe and fast way. Nowadays, it uses modern technologies as the computer tomography and rapid prototyping, and it represents significant example of integration among different areas of the knowledge. This work presents the medical modeling and discusses its applications, with emphasis in the integration of the technologies of rapid prototyping, reverse engineering (RE) and computer aided design and engineering (CAD/CAE). It is made a description of the procedures to generate the medical models using rapid prototyping techniques starting from computer tomography data, and a study regarding the dimensional and geometric precision of the medical models generated by rapid prototyping. The advantages of the integration with CAD/CAE technologies are shown and a case study is developed aiming to validate the proposed procedures.

A modelagem de geometrias da natureza pode ser um processo complexo devido ás características orgânicas dos elementos. Propõe-se com essa dissertação identificar geometrias espaciais que sigam o padrão de crescimento espiral observado na natureza, utilizando as Tecnologias 3D como ferramentas para o processo de projeto. Para a execução do trabalho foram investigadas os Métodos de Biônica, Crescimento Espiral e a Sequência de Fibonacci, Engenharia Reversa e Design Paramétrico. O processo de representação dos elementos foi realizado em conformidade com a Metodologia para o Desenvolvimento de Produtos Baseados no Estudo da Biônica com o acréscimo das tecnologias de digitalização tridimensional e de processamento de nuvem de pontos, complementado pela parametrização de superfícies à base de curvas. Foram utilizados três processos para modelagem de curvas paramétricas representadas (i) pelo desenho de linhas sobre a malha digitalizada em 3D, (ii) por programação visual no software Grasshopper e (iii) por programação com scripts Python. Foi avaliada como melhor alternativa para o Design Paramétrico a utilização da programação visual otimizada com a programação por scripts, a qual apresentou melhor aproximação entre as curvas analisadas. Estudos de casos realizados com elementos da natureza (abacaxi e pinha) demonstraram a viabilização do método. Desta maneira a sistematização do conhecimento permitirá a proposição de um modelo paramétrico baseado na Biônica para fase inicial de inspiração e concepção de alternativas do projeto de produto. / Modeling the geometries of nature can be a complex process due to the organic characteristics of the elements. It is proposed with this dissertation to identify spatial geometries that follow the pattern of spiral growth observed in nature, using 3D Technologies as tools for the design process. For the execution of the work were investigated the Bionics, Spiral Growth and Fibonacci Sequence, Reverse Engineering and Parametric Design. The process of representation of the elements was carried out in accordance with the Methodology for the Development of Products Based on the Study of the Bionics with the addition of the technologies of three-dimensional digitization and processing of cloud of points, complemented by the parameterization of surfaces based on curves. Three methods were used for modeling parametric curves represented by (i) the drawing of lines on the 3D scanned mesh, (ii) by visual programming in the Grasshopper software and (iii) by programming with Python scripts. It was evaluated as the best alternative for Parametric Design the use of optimized visual programming with programming by scripts, which presented better approximation between the analyzed curves. Case studies carried out with nature elements (pineapple and pine cone) demonstrated the viability of the method. In this way the systematization of the knowledge will allow the proposition of a parametric model based on the Bionics for the initial phase of inspiration and design of alternatives of the product design.

La modernisation logicielle est un domaine en plein essor du fait du vieillissement des technologies datant des années 1960, tel que COBOL ou FORTRAN. Aujourd'hui, bon nombre de ces applications sont toujours en service du fait de leur criticité. Ce sont elles qui continuent d'assurer le bon fonctionnement du système d'information de l'entreprise. Face à l'arrivée en force de technologies récentes de type Cloud ou Mobile, il devient urgent de les moderniser. Toutefois, près de deux projets de modernisation sur trois échouent à cause du manque ou la perte de documentation de l'application, la complexité du logiciel (qui lui n'a cessé de grandir avec le temps), la perte des connaissances techniques (les jeunes développeurs n'ont jamais étudié ces anciennes technologies), tout cela couplé à un manque d'outils et de méthodes industrielles. Face à ce constat implacable, cette thèse suggère une solution pour l'industrialisation du processus de modernisation à travers l'utilisation de l'Ingénierie Dirigée par les Modèles (IDM), notamment en prenant pour base les métamodèles issus de l'initiative Architecture Driven Modernisation de l'OMG. Nous montrons qu'il est ainsi possible d'automatiser une majorité du processus du fait de l'utilisation de métamodèles pivots technologiquement neutres, ainsi que l'utilisation d'une série d'outils permettant d'obtenir une automatisation des tâches de migration de l'application. Nous proposons également de rendre cette solution adaptable à n'importe quel langage légataire au travers d'une chaîne de modernisation paramétrable via l'utilisation d'un moteur de transformation dédié offrant des mécanismes d'extensibilité et de réutilisabilité. Pour terminer, nous illustrons l'ensemble des idées développées dans cette thèse sur l'exemple concret d'une application codée en COBOL. / Software modernization is a fast-growing sector due to the aging technologies from the 1960s, such as COBOL or FORTRAN. Nowadays, many of these applications are still being used because of their criticality. These applications allow companies to maintain their information system. But to face the arrival of newer technologies and platforms, like Cloud or Mobile, companies must modernize their systems to deliver the same services and also develop new ones in order to compete. However, nearly two out of three modernization projects fail because of the lack or the loss of applications documentation, the complexity of the software (that has continued to grow over time), the loss of technical knowledge (the junior developers have never studied these ancient technologies), plus a lack of tools and industrial methods. Faced with this relentless observation, this thesis suggests a solution to the industrialization process of modernization through the use of Model Driven (IDM) Engineering, especially by using metamodels base from Driven Architecture Modernization of the OMG. We therefore demonstrate that it is possible to automate the process thanks to technologically neutral metamodels and by using a set of tools to get the automation of application migration tasks. We also propose to have this solution adapted to any languages through a configurable chain of modernization by using a dedicated processing engine that provides scalability and reusability mechanisms. Finally, we illustrate the ideas developed in this thesis in the concrete case of a coded COBOL application.

Um método composto de quatro passos para conduzir engenharia reversa orientada a objetos de sistemas desenvolvidos sem usar a tecnologia de orientação a objetos e apresentado. Este método abrangente e detalhado mostrando como fazer engenharia reversa constitui um avanço para o estado da arte, pois não há métodos publicados nesse nível de detalhe ate o momento. A documentação produzida pela engenharia reversa baseada no Método Fusion para desenvolvimento de sistemas orientados a objetos e composta de um Modelo de Objetos, um Modelo de Operação e um Modelo de Ciclo de Vida. Um conjunto de modelos intermediário extraído diretamente do código e dos documentos de interação processo/dados e também incluído com o nome de Modelo de Análise do Sistema Atual. A engenharia reversa de um ambiente de software para projetar sistemas reativos e mostrada em detalhes. Esse software tem 30.000 linhas de código C, divididas em 495 procedimentos agrupados em 36 módulos. Um documento semelhante a um dicionário de dados foi preparado com base na documentação contida em diversas dissertações, artigos e principalmente em seu código fonte. O ambiente de desenvolvimento de sistemas reativos e descrito, bem como sua evolução através de diversas versões e sua aplicação e ilustrada pelo projeto do statechart correspondente a um relógio despertador. Facilidades para especificar atividades associadas aos statecharts foram incorporadas ao ambiente StatSim como parte dos trabalhos desenvolvidos nesta tese e são também discutidas e aplicadas a um exemplo. A simulação de statecharts de controle sujeitos a diferentes eventos possíveis e incluída através de diagramas e \"logs\". Esse exemplo é também usado para ilustrar um procedimento relacionado ao acoplamento de statercharts e diagramas de atividades na especificação de sistemas reativos e para mostrar o uso do ambiente de software para verificar essa especificação. O Método Fusion e comparado a outros métodos de desenvolvimento de sistemas orientados a objetos. O ambiente de desenvolvimento de sistemas reativos baseado em statecharts e posicionado entre outras ferramentas para o desenvolvimento de tais sistemas. / A method composed of four steps to conduct object oriented reverse engineering in systems developed using non object oriented technology is presented. This comprehensive, detailed method showing how to do reverse engineering is an advance to the state of the art as there are no published methods hitherto at this level of detail. The documentation produced by the reverse engineering based on the Fusion Method for object oriented systems development is composed by an Object Model, an Operation Model and a Life Cycle Model. An intermediary set of models directly extracted from the code and from a process/data interaction document is also included with the name of Current Systems Analysis Model. The reverse engineering of a software environment for designing reactive systems is shown in detail. This software comprises 30.000 lines of code in C, spread for 495 procedures grouped in 36 modules. This data dictionary-like document was prepared based on documentation contained in several dissertations and papers and mainly on the code itself. The reactive systems software development environment is described as well as its evolution through several versions, and its application is illustrated by designing the statecharts corresponding to an alarm clock. Facilities to specify activities triggered by the statecharts incorporated to the StatSim environment as part of this thesis\' are also discussed and applied to the example. The simulation of the controlling statecharts subjected to different possible events is included through diagrams and logs. This example is also used to illustrate a procedure devised for coupling statecharts and activity diagrams in the specification of reactive systems and for using the software environment to verify this specification. The Fusion Method is compared to other methods for object oriented systems development. The reactive systems development environment based on statecharts is situated among other tools for the development of such systems.