"As software systems become more complex, so does the task of understanding them. To modify even a simple component of a complex system, at least a rudimentary understanding of the structure and behavior of the whole system is necessary. Although currently available development tools can provide a static representation of a complex system, these utilities are severely limited and prohibitively expensive. As a result, most programmers working on large software systems today resort to classic debuggers and time-consuming plain-text searches through hundreds or thousands of source files. This proposal describes a software development environment that uses static representations of hierarchically structured source code side by side with dynamic visualizations of software systems as they run. This environment provides an intuitive, visual means of easily comprehending complex systems, and has been provided as an open-source development tool for both professionals and students of software engineering."

O surgimento e a popularização de arquiteturas de software que fornecem suporte à programação distribuída orientada a objetos, como CORBA, .NET e Java EE, gerou uma demanda por infra-estruturas de segurança eficientes, capazes de proteger os recursos dos sistemas de ataques maliciosos. Essa proteção começa pela identificação dos usuários que interagem com os sistemas, processo conhecido como autenticação. Entretanto, a autenticação por si só não é suficiente para garantir a segurança dos recursos, uma vez que a autenticação não determina quais ações os usuários estão autorizados a executar depois de autenticados. Em outras palavras, um mecanismo de autorização, que faz valer as políticas de controle de acesso aos recursos definidas pelos administradores de sistemas, se faz necessário. Neste trabalho estudamos mecanismos de controle de acesso baseado em papéis e a aplicabilidade dos certificados de atributos X.509 como estrutura de armazenamento desses papéis em um ambiente Java EE. Em particular, estendemos a infra-estrutura de segurança do servidor de aplicações JBoss, de modo que ela passasse a comportar os certificados de atributos X.509. Além disso, analisamos as vantagens e desvantagens do uso de tais certificados e avaliamos o desempenho da extensão desenvolvida em relação a outras alternativas que são oferecidas pelo JBoss para o armazenamento de papéis dos usuários. / The popularization of software architectures that provide support for distributed object-oriented programming, like CORBA, .NET, and Java EE, revealed the need for efficient security infrastructures to protect the resources of enterprise systems from malicious attacks. This protection usually begins with the identification of the users that interact with the systems, a process known as authentication. However, authentication alone is not enough to guarantee the protection of the resources, as it cannot determine what actions a particular user is allowed to execute on a given resource. In other words, an authorization mechanism is needed in order to enforce the access control policies as defined by the system administrators. In this dissertation we studied role-based access control mechanisms and the use of X.509 attribute certificates as data structures that store the users roles in a Java EE environment. Particularly, we added X.509 attribute certificates support to the existing JBoss application server security infrastructure. Furthermore, we evaluated the pros and cons of using these certificates, and compared the performance of the developed extension to the performance of the existing solutions provided by JBoss to store the users roles.

Este projeto de pesquisa trata da elaboração de um sistema de reconstrução de imagens obstétricas de fetos, em aparelhos de ultra-som convencionais, para a visualização dessas imagens em três dimensões utilizando a internet como meio de utilização do sistema, com o principal objetivo de proporcionar aos médicos ginecologistas melhor visualização do formato e das estruturas internas, e em especial da face do feto, através do processo de reconstrução tridimensional feito a partir de um conjunto de imagens bidimensionais capturadas em aparelhos convencionais de ultra-som. O uso clínico deste projeto está previsto para o setor de obstetrícia do Hospital das Clínicas de Ribeirão Preto. / This project of research deals with the laboration of a reconstruction system of obstetrics images of embryos in devices of ultrasound will be conventional the visualization of these images in three dimensions using the internet half of uses of the system, with the main objective provides to the medical gynecologists a better visualization of the format and the internal structures and in special the face of the embryo through the made process of three-dimensional reconstruction from a dataset of captured bi-dimensional images in conventional devices of ultrasound. The clinical uses of this project is foreseen will be the sector of obstetrics of the Hospital of the Clinics of Ribeirão Preto.

Com a presença cada vez maior de sistemas computacionais e novas tecnologias no cotidiano das pessoas, garantir que eles não falhem e funcionem corretamente tornou-se algo de extrema importância. Além de indicar a qualidade do sistema, assegurar seu bom funcionamento é essencial para se evitar perdas, desde financeiras até de vidas. Uma das técnicas utilizadas para esta finalidade é a chamada verificação formal de programas. A partir da especificação do sistema, descrita numa linguagem formal, são definidas propriedades a serem satisfeitas e que certificariam a qualidade do software. Estas propriedades devem então ser implementadas para uso num verificador, que é a ferramenta responsável por executar a verificação e informar quais propriedades foram satisfeitas e quais não foram; no caso das propriedades terem sido violadas, o verificador deve indicar aos desenvolvedores os possíveis locais com código incorreto no sistema. A desvantagem do uso da verificação formal é, além do seu alto custo, a necessidade de haver pessoas com experiência em métodos formais para definir propriedades a partir da especificação formal do sistema, e convertê-las numa representação que possa ser entendida pelo verificador. Este processo de definição de propriedades é particularmente complexo, demorado e suscetível a erros, por ser feito em sua maior parte de forma manual. Para auxiliar os desenvolvedores na utilização da verificação formal em programas escritos em Java, propomos neste trabalho a geração de representação de propriedades para uso direto num verificador. As propriedades a serem geradas são objetivos de teste derivados da especificação formal do sistema. Estes objetivos de teste descrevem o comportamento esperado do sistema que deve ser observado durante sua execução. Ao estabelecer que o universo de propriedades corresponde ao universo de objetivos de teste do programa, garantimos que as propriedades geradas em nosso trabalho descrevem o comportamento esperado do programa por meio de caminhos de execução que levam a um estado de aceitação da propriedade, ou a um estado de violação. Assim, quando o verificador checa o objetivo de teste, ele consegue dar como resultado o veredicto de sucesso ou falha para a propriedade verificada, além de dados da cobertura dos caminhos de execução do programa que podem ser usados para análise do comportamento do programa que levou ao sucesso ou falha da propriedade verificada. / The task of guaranteeing that computational systems do not fail and work correctly has become extremely important with the growing presence of new technologies in people\'s lives. Therefore, it is essential to ensure that such systems work properly to confirm their high-quality and to avoid financial and even life losses. One of the techniques used to this purpose is called formal verification of programs. From the system specification, which should be described in a formal language, we define properties that must be satisfied during system execution to guarantee the software quality. Then, these properties are checked using a verifier, which is the tool responsible for running the verification and for notifying whether the property was satisfied by the program; if the property was violated, it indicates to software developers the possible location of faults in the system. The disadvantages of using formal verification are the high cost to apply this technique in practice, and the necessity of having people with experience in formal methods to derive the properties from system specification and define them in a formal representation that can be read by a program verifier. This particular task of deriving a property from system specification and defining it to be checked by a verifier is complex, time-consuming and error-prone, since it is usually done by hand. To help software developers in the application of formal verification in Java programs, we propose in this work the generation of properties formal representation for direct use in a verifier. The generated properties are test purposes, which are derived from system formal specification and present the desirable system behavior that must be observed during the system execution. Establishing that the universe of properties correspond to the universe of test purposes of a program, we guarantee that the generated properties describe the expected program behavior through execution traces that lead to either an accept state or a refuse state. Thus, when the verifier checks the test purpose, it can give a success/fail verdict for the property, and provide traces coverage data that can be used to analyze the program behavior that led to that verdict.

Grades Computacionais (grid computing) já é uma realidade tanto no meio acadêmico quanto no meio empresarial. Seu uso se tornou popular principalmente devido à divulgação dos trabalhos nesta área e pela propaganda de produtos e softwares que oferecem essa idéia. Apesar disso, ambientes para o desenvolvimento de aplicações orientadas a objetos em Java para uma infra-estrutura de grid ainda é escasso. Algumas iniciativas oferecem bibliotecas para este desenvolvimento. Outras utilizam paradigmas diferentes, como o de passagem de mensagem, para o desenvolvimento de aplicações. Além disso, a própria infra-estrutura de grid, formada por diferentes domínios administrativos com diferentes políticas de segurança e uso, impede que as aplicações sejam executadas nos diversos níveis existentes no grid. Estes níveis, formados por computadores e clusters de computadores com nós de execução, possuem endereçamento privado, impossibilitando que as aplicações alocadas em cada um desses computadores/nós, em diferentes domínios e diferentes endereços, se comuniquem de forma transparente. Visando uma solução para esses problemas, esta tese apresenta um ambiente para programação orientada a objetos distribuídos e paralelos, em Java, denominado J4GE. Nesse ambiente, o modelo orientado a objetos é base para a distribuição das classes, métodos e atributos existente em uma aplicação. Além disso, o ambiente oferece transparência no acesso aos objetos espalhados pelo grid através de um Serviço de Mensagem, independente do nível onde o recurso, computador ou nó, se encontra. Essa transparência permite também que o programador utilize a plataforma Java sem a necessidade de aprender ou conhecer novas bibliotecas ou paradigmas, diminuindo o esforço no desenvolvimento de aplicações para grid. E, juntamente com os recursos da plataforma Java e do ambiente J4GE, é possível criar objetos distribuídos com comportamento paralelo e concorrente, trazendo maior eficiência para a execução da aplicação. / Grid computing is already a reality both in academic and business world. Its use has become popular mainly because of the projects in this area and the advertising of products and software that offer this idea. Nevertheless, environments for development of object-oriented applications in Java for grid infrastructure are still scarce. Some initiatives offer libraries for this development. Others use different paradigms such as the message-passing for development of applications. Moreover, the infrastructure of grid, formed by different administrative domain with different security policies, prevents the execution of applications at various levels in the grid. These levels, formed by computers and clusters of computers with execution nodes, have private addresses, make impossible the transparent communication of the applications allocated in each of these computers at different levels in different domains. Focused on these problems, this thesis presents an environment for distributed and parallel object-oriented programming in Java, called J4GE. In this environment, the object-oriented model is the basis for the distribution of classes, methods and attributes in an existing application. Moreover, the environment offers transparency in objects access around the grid through a Message Service, regardless the level where is the resource, or the computer, or the execution node. This transparency also allows the programmer to use the Java platform without knowing or learning new libraries or paradigms, reducing the effort in developing applications for grid. The resources of the Java platform and the environment J4GE together can create distributed objects with parallel and concurrent behavior, bringing greater efficiency to the application.

O teste de programas concorrentes é uma atividade que envolve diferentes perspectivas. Uma das mais conhecidas refere-se ao desenvolvimento de novos conhecimentos sobre critérios, modelos e ferramentas de teste que auxiliem o testador nessa atividade. Outra perspectiva, igualmente importante, porém, ainda incipiente, é a avaliação da atividade de teste de programas concorrentes com relação à sua eficiência e eficácia para revelar defeitos de difícil detecção. O projeto TestPar em desenvolvimento no ICMC/USP tem abordado essas duas perspectivas ao longo dos últimos anos, onde novas tecnologias de teste vêm sendo desenvolvidas e avaliadas sistematicamente. Este trabalho inseriu-se no contexto do projeto TestPar e teve por objetivo principal contribuir para melhorar a avaliação da atividade de teste de programas concorrentes, através do desenvolvimento de benchmarks específicos para este contexto. Essa avaliação representa um desafio para a área de teste, sendo essencial a existência de benchmarks simples o bastante para serem validados manualmente, se necessário, e complexos o bastante para exercitar aspectos não triviais de comunicação e sincronização, encontrados de fato nos programas concorrentes. Assim, neste trabalho de mestrado foram desenvolvidos benchmarks livres de defeitos conhecidos e algumas versões de benchmarks com defeitos intencionalmente inseridos, baseados em taxonomias de defeitos. Esses benchmarks seguiram uma série de características bem definidas, contando ainda com uma documentação padronizada e completa. Os benchmarks foram validados através da condução de estudos experimentais, do uso em diferentes projetos de pesquisa e também com a verificação da sua aplicabilidade para fins educacionais. Os resultados obtidos demonstram que os benchmarks atingiram os objetivos para os quais foram propostos, gerando uma demanda controlada e qualificada sobre modelo, critérios e a ferramenta de teste desenvolvidos no projeto TestPar. Os experimentos realizados permitiram destacar pontos positivos e limitações desses artefatos. Outra aplicação dos benchmarks foi como recurso educacional para o ensino em disciplinas como programação concorrente. / The testing of concurrent programs is an activity that involves distinct perspectives. One of the most known refers to the development of new knowledge about criteria, models and testing tools to support this activity. Other perspective, as important as the first one and still incipient, is the evaluation of the testing activity of concurrent programs with respect to its efficiency and effectiveness in revealing errors hard to detect. The TestPar project under development at ICMC/USP has addressed both these two perspectives over the past years, where new testing technologies are being proposed and evaluated systematically. This project belongs to the context of the TestPar project, aiming to improve the evaluation of the testing activity of concurrent programs through the development of benchmarks specific for this context. This evaluation represents a challenge to the testing area, which must consider benchmarks simple enough to be validated manually, if necessary, but also complex enough to exercise not trivial aspects of communication/synchronization, found in programs used indeed. Thus, in this work it were developed bug-free benchmarks and some versions of faulty benchmarks with bugs inserted, based on error taxonomies. These benchmarks followed a series of well-defined features, including also a standardized and complete documentation. Benchmarks were validated by means of diferent scenarios: experimental studies, their use by different on-going research projects and also with the verification of their applicability for educational aims. The results obtained show that our benchmarks have achieved their objectives, generating a controlled and qualified demand on model, criteria and the tool developed under TestPar project. The experiments reveal strengths and limitations of these artifacts. Benchmarks have been also used as educational resources for the teaching of concurrent programs.

O objetivo deste trabalho é avaliar a recuperação de imagem por conteúdo (CBIR - Content-based Image Retrieval) em uma rede de computadores, estabelecendo-se métricas de controle que otimizem a utilização da rede e ao mesmo tempo garanta melhor qualidade na resposta. Prevê-se a recuperação de imagens baseada em consulta por similaridade, combinando-se o extrator de características com a função de distância. O desenvolvimento é realizado em uma linguagem de programação independente da plataforma e de âmbito de internet, utilizado Java, desenvolvendo-se uma API (Application Programming Interface), visando, em especial, a reutilização de código, o que implica na diminuição do tempo de desenvolvimento. O trabalho demonstra a utilização de estruturas de indexação sequencial, comparada com a estrutura de indexação de árvore \"Slim-tree\". A principal contribuição deste trabalho é a análise e a utilização de métricas na rede de computadores em um projeto de CBIR. / The objective of this study is to evaluate the Content-based Image Retrieval (CBIR) in a computer network, establishing control metrics that optimize the use of network while ensuring better quality in the response. It is expected that images are going to be recovered based on queries that are similar, combining the features extractor with the distance function. The development environment is an independent language of the platform and of the Internet scope, using Java, that has developed an Application Programming Interfaces (API), aiming primarily the code reuse, which implies a decrease in the development time. This thesis demonstrates the use of sequential indexing structures compared to the tree index structure \"Slim-tree\". The main contribution of this thesis is the analysis and utilization of metrics in a computer network project in CBIR.

<p>Detta examensarbete är framtaget för att utforma moduler till programmet BioSpider som utvecklats vid ADIT avdelningen vid IDA institutionen Linköping Universitet med syfte att förenkla för biologer när de söker information om andra forskares resultat.</p><p>Det finns ett stort antal databaser som innehåller forskningsdata kring proteiner, reaktioner, signalvägar etc. Exempel på databaser är UniProt, Reactome, IntAct, BioModels och KEGG. Det uppstår problem med att dessa databaser är uppbyggda på olika sätt och ej kan användas på ett universellt sätt, utan kräver individuellt utformning och anpassning för att kunna användas tillsammans med andra databaser.  Det är där BioSpider kommer in, BioSpider är ett program som försöker bygga upp ett träd utifrån olika databaser. Varje databas hanteras individuellt av BioSpider men presenteras på ett universellt sätt i form av ett träd för användaren. Examensarbetets del i BioSpider är att utforma moduler som behandlar ytterligare databaser utöver BioModels som redan stöds i BioSpider.</p><p>Behovet av att tillgängliggöra stöd för fler databaser var nödvändigt för att kunna visa upp en användbar version av BioSpider med mer än en databas. Detta för att kunna visa att metoden fungerar i praktiken.</p><p>Examensarbetet har utförts genom att en förstudie av ett antal databaser har gjorts och inom dessa valt ut relevant information som sedan implementerats i BioSpider med olika moduler för de olika databaserna.</p><p>Det som fanns tillgängligt vid examensarbetets start var programmet BioSpider och implementation för en databas (BioModels). Nu stöds BioSpider av ytterligare fyra stycken databaser som är UniProt, Reactome, KEGG och IntAct som bygger ut trädet. BioSpider stöds även utav DIP, Ensembl, EMBL, FlyBase, GO, InterPro, OMIM, PDB, PIR, PROSIT och RefSeq för vidare länkning till webbsida där ytterligare information kan återfås.</p> / <p>The aim of this thesis was to develop modules for the system BioSpider that are developed by ADIT division at IDA institute at Linköping University. The objective is to simplify for biologist when they seek for information about research findings.</p><p>There is a large number of databases that contains research results about proteins, reactions, pathways etc. Examples of these databases are UniProt, Reactome, IntAct, BioModels and KEGG. Problems emerges since the databases are constructed in different ways and cannot be used in a universal way, they must be individually tailored and adjusted to be compatible with other databases. This is where BioSpider comes in, BioSpider is a program that is supposed to build up a tree of the different databases. Each database is managed individually by BioSpider and is presented to the user in a universal way in the form of a tree. This thesis extends the BioSpider system so that more databases are supported than just the database BioModels.</p><p>The need to support more databases was necessary to be able to produce a usable version of BioSpider with more than one database. This is important to show that the method works in practice.</p><p>The work has been performed by a pilot study of a number of databases. Within these we selected appropriate information that was implemented in BioSpider with different modules for different databases.</p><p>At start of this thesis one database was supported by BioSpider, this database is BioModels. Now BioSpider supports by additional four databases UniProt, Reactome, KEGG and IntAct. BioSpider also supports linking to websites where information can be retrieved, the supported databases are DIP, Ensembl, EMBL, FlyBase, GO, InterPro, OMIM, PDB, PIR, PROSIT and RefSeq.</p>

This study is an attempt to measure religious fertility differentials of the Abangan and the Santri, two different Muslim groups on Java. The Santri are those who strongly endeavor to carry out the religious prescriptions and observances; the Abangan, on the other hand, are individuals whose religious orientation is not as strong. The main purpose of the study is to determine if religion explains the high fertility level on Java. The results are expected to be important for the population policy makers enabling them to determine the factors influencing fertility level in the area studied.Studies of the literature lead to the formation of the theory employed for the study, which is a hybrid: drawing elements from four theoretical explanations of religious differences in fertility. It maintains that religious doctrine affiliation interacts with socioeconomic factors in explaining fertility. Three stages of socioeconomic level are assumed: (1) traditional; (2) transitional; and (3) modern. The study hypothesizes that religious fertility differentials of the two groups are slight when they are in the traditional stage. Further, the Santri are predicted to maintain higher fertility level than the Abangan.The data accessed for the study are from a 1974-1975 study on transmigration on Java. The sampling procedure was a stratified probability random sampling, with 3000 individuals of rural and urban areas on Java. One major weakness encountered in the data is the lack of detailed information on fertility determinants such as contraceptive use, marriage duration, and age of wife at first marriage.Among other things, one factor that justifies the use of the data is the extensive information religious practices of the people.Multiple regression analyses are conducted to test the hypotheses of the study. The data is analyzed by computer using the SPSS (Statistical Package for Social Sciences) program. The significant test employed to measure the impact of the independent variables on the dependent variables is the F test.Taking into consideration that the majority of the respondents are from a low socioeconomic level and rural residents, the stage being observed in this study is the traditional one. Two measures are employed to determine fertility, namely, number of children ever born and ideal family size preferred by married couple when they started the household.Factors employed to explain the fertility levels are religious group affiliation, education, wife's age, and income. The study found little significant difference on the cultural and in the fertility level of the two groups. However, with additional analysis it was found further that the interaction of religious doctrine affiliation and wife's education correlates significantly with the ideal family size preferred, but not with the number of children ever born.The insignificant difference of the fertility levels of the two groups is rather surprising. One possible explanation for the case is the discrepancy between the theoretical definition of the two religious groups and the empirical phenomena. As a matter of fact, the Muslim groups on Java are not as clearly distinguishable as suggested in this study. The discrepancy results in the inaccuracy of the data analysis, for those who in the study are considered as belong to the Abangan category are actually residual cases of the Santri category. Hence, analyses are not accurate. Had the two groups been measured based on the theoretical concepts, the results of the study could possibly be as expected.Although the study is limited in its intensity, the results are valuable for future studies. It is recommended that other factors such as cultural values, information pertaining to birth control , and family planning be considered for future studies. Specific measurement of religious groups studied would yield a better explanation on religious fertility differential.

This report presents the SHAP platform consisting of its microarchitecture and its implementation of the Java Virtual Machine (JVM). Like quite a few other embedded implementations of the Java platform, the SHAP microarchitecture relies on an instruction set architecture based on Java bytecode. Unlike them, it, however, features a design with well-encapsulated components autonomously managing their duties on rather high abstraction levels. Thus, permanent runtime duties are transferred from the central computing core to concurrently working components so that it can actually spent a larger fraction of time executing application code. The degree of parallelity between the application and the runtime implementation is increased. Currently, the stack and heap management including the automatic garbage collection are implemented this way. After detailing the design of the microarchitecture, the SHAP implementation of the Java Virtual Machine is described. A major focus is laid on the presentation of the layout and the use of the runtime data structures representing the various language abstractions provided by Java. Also, the boot sequence starting the JVM is described.