Software architecture provides a high-level framework for a software system, and plays an important role in achieving functional and non-functional requirements. Since the year 2004, software architecture has been considered as a set of architectural design decisions (ADDs). However, software architecture is implicit and evolves as the software development process moves forward. The implicitness together with continuous evolution leads to many problems such as architecture drift and erosion as well as high cost reconstruction. Without capturing and managing ADDs, most of existing architectural knowledge evaporates, and reusing and evolving architecture can be difficult. These problems are even more serious in global software development (GSD). This dissertation presents a novel methodology for capturing ADDs during the architecting process and managing the evolution of ADDs to reduce architectural knowledge evaporation. This methodology explicitly documents ADDs using a scenario-based approach, which covers three views of a software architecture, to record architectural knowledge, and incorporates evolution-centered characteristics to manage ADD evolution for reducing architectural knowledge evaporation. Furthermore, the dissertation presents ADD management in the context of GSD to analyze typical ADD management paradigms, and to offer insights on, techniques on, and support for sharing and coordinating ADDs in a GSD setting. This dissertation focuses on both the documentation and the evolution needs for ADDs in localized and global software development. / text

Software architecture is considered as a set of architectural design decisions. Capturing and representing architectural design decisions during the architecting process is necessary for reducing architectural knowledge evaporation. Moreover, managing the evolution of architectural design decisions helps to maintain consistency between requirements and the deployed system. In this thesis, we create the Triple View Model (TVM) as a general architecture framework for documenting architectural design decisions. The TVM clarifies the notion of architectural design decisions in three different views and covers key features of the architecting process. Based on the TVM, we propose a scenario-based methodology (SceMethod) to manage the documentation and the evolution of architectural design decisions. We also conduct a case study on an industrial project to validate the applicability and the effectiveness of the TVM and the SceMethod. The results show they provide complete documentation on architectural design decisions for creating a system architecture, and well support architecture evolution with changing requirements. / text

Diversos negócios hoje são suportados por sistemas de software. Acredita-se que o uso de Arquitetura de Software é fundamental para atingir alcançar as metas de negócio e qualidade. Visto que o conjunto de requisitos que levou à construção de uma determinada arquitetura pode mudar, tal arquitetura pode tornar-se inadequada. Em diversas situações é preciso conviver com os sistemas existentes, portanto é preciso alterá-los para as novas necessidades. Manutenção de sistemas usando técnicas de evolução arquiteturais tem se mostrado um eficaz caminho para alterar um sistema à nova situação. O objetivo deste trabalho é apresentar um método para manutenção de sistemas de software usando técnicas arquiteturais de forma a convergir mais rapidamente à adequação da arquitetura destes sistemas. Algumas técnicas do método incluem avaliação de arquitetura de software, levantamento de riscos, provas de conceito construtivas e destrutivas e métricas estáticas e dinâmicas de software. O método proposto foi aplicado em contextos de laboratório e da indústria, permitindo a verificação de pontos fortes e críticos para realizar seu refinamento e tais aplicações são também relatadas neste trabalho. Embora as aplicações do método proposto tenham sido diferentes, tanto no objetivo principal quanto no desenrolar das atividades, seus resultados foram considerados bastante satisfatórios, tanto no contexto de ensino quanto no contexto de indústria. / Several business today are supported by software systems. It is believed that the use of software architecture is fundamental to achieve the business goals and quality. Since the set of requirements that led to the construction of a given architecture may change, such an architecture may become inadequate. In many situations we must live with existing systems, so we must change them to meet the new needs. Systems maintenance using architectural evolution techniques has proven to be an effective path to take a system to the new situation. This works goal is to provide a method for maintenance of software systems using architectural techniques in order to converge more rapidly to match the architecture of these systems. Some techniques used in the method include software architecture evaluation, risks survey, constructive and destructive proofs of concept, static and dynamic software metrics. The proposed method was applied in contexts of laboratory and industry, allowing the verification of strengths and critical points to guide its refinement and such applications are also reported in this work. Although the applications of the proposed method has been different in both the main goal and the conduct of activities, their results were considered very satisfactory, both in the education and the industry context.

Diversos negócios hoje são suportados por sistemas de software. Acredita-se que o uso de Arquitetura de Software é fundamental para atingir alcançar as metas de negócio e qualidade. Visto que o conjunto de requisitos que levou à construção de uma determinada arquitetura pode mudar, tal arquitetura pode tornar-se inadequada. Em diversas situações é preciso conviver com os sistemas existentes, portanto é preciso alterá-los para as novas necessidades. Manutenção de sistemas usando técnicas de evolução arquiteturais tem se mostrado um eficaz caminho para alterar um sistema à nova situação. O objetivo deste trabalho é apresentar um método para manutenção de sistemas de software usando técnicas arquiteturais de forma a convergir mais rapidamente à adequação da arquitetura destes sistemas. Algumas técnicas do método incluem avaliação de arquitetura de software, levantamento de riscos, provas de conceito construtivas e destrutivas e métricas estáticas e dinâmicas de software. O método proposto foi aplicado em contextos de laboratório e da indústria, permitindo a verificação de pontos fortes e críticos para realizar seu refinamento e tais aplicações são também relatadas neste trabalho. Embora as aplicações do método proposto tenham sido diferentes, tanto no objetivo principal quanto no desenrolar das atividades, seus resultados foram considerados bastante satisfatórios, tanto no contexto de ensino quanto no contexto de indústria. / Several business today are supported by software systems. It is believed that the use of software architecture is fundamental to achieve the business goals and quality. Since the set of requirements that led to the construction of a given architecture may change, such an architecture may become inadequate. In many situations we must live with existing systems, so we must change them to meet the new needs. Systems maintenance using architectural evolution techniques has proven to be an effective path to take a system to the new situation. This works goal is to provide a method for maintenance of software systems using architectural techniques in order to converge more rapidly to match the architecture of these systems. Some techniques used in the method include software architecture evaluation, risks survey, constructive and destructive proofs of concept, static and dynamic software metrics. The proposed method was applied in contexts of laboratory and industry, allowing the verification of strengths and critical points to guide its refinement and such applications are also reported in this work. Although the applications of the proposed method has been different in both the main goal and the conduct of activities, their results were considered very satisfactory, both in the education and the industry context.

Lacking experimental data, protein function is often predicted from evolutionary and protein structure theory. Under the 'domain grammar' hypothesis the function of a protein follows from the domains it encodes. Under the 'orthology conjecture', orthologs, related through species formation, are expected to be more functionally similar than paralogs, which are homologs in the same or different species descended from a gene duplication event. However, these assumptions have not thus far been systematically evaluated. To test the 'domain grammar' hypothesis, we built models for predicting function from the domain combinations present in a protein, and demonstrated that multi-domain combinations imply functions that the individual domains do not. We also developed a novel gene-tree based method for reconstructing the evolutionary histories of domain architectures, to search for cases of architectures that have arisen multiple times in parallel, and found this to be more common than previously reported. To test the 'orthology conjecture', we first benchmarked methods for homology inference under the obfuscating influence of low-complexity regions, in order to improve the InParanoid orthology inference algorithm. InParanoid was then used to test the relative conservation of functionally relevant properties between orthologs and paralogs at various evolutionary distances, including intron positions, domain architectures, and Gene Ontology functional annotations. We found an increased conservation of domain architectures in orthologs relative to paralogs, in support of the 'orthology conjecture' and the 'domain grammar' hypotheses acting in tandem. However, equivalent analysis of Gene Ontology functional conservation yielded spurious results, which may be an artifact of species-specific annotation biases in functional annotation databases. I discuss possible ways of circumventing this bias so the 'orthology conjecture' can be tested more conclusively. / At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 6: Epub ahead of print.