Refactorings to evolve object-oriented systems with aspect-oriented concepts

Tese de doutoramento em Informática.Software engineering tools should support complete separation of concerns, by enabling the deployment of each different concern in its own unit of modularity. Unfortunately, current tools and languages – including those supporting the object-oriented programming paradigm – fail to provide a complete and effective support for the separation of all concerns. Undesirable phenomena such as code scattering and code tangling ensue. Aspect-Oriented Programming is a new programming paradigm capable of modularising crosscutting concerns. Aspect-oriented programming complements existing programming paradigms, including object-oriented programming, with constructs that provide a fuller separation of concerns. Refactoring is a technique to restructure program source code in order to improve its underlying design and style while preserving the externally observable behaviour. “Code smells” help to detect inadequate structures and designs, which are then gradually removed through refactoring processes. There is a prospect of aspect-oriented programming becoming a mainstream technology in the near future. This begs the question of how to deal with a large base of object-oriented legacy code when aspect-orientation becomes standard practice. AspectJ's backward compatibility with Java opens the way for refactoring existing Java applications to leverage the concepts and mechanisms of aspects. This requires a prior idea of good style for aspect-oriented source code, something yet to be developed and matured. This thesis contributes to the definition of a new style appropriate to aspect orientation. To this effect, this thesis documents a collection of novel refactorings enabling the extraction of crosscutting concerns from object-oriented legacy source code and the subsequent restructuring of the aspects thus obtained. In addition, this thesis presents a review of traditional object-oriented code smells so they can be used as indicators of latent aspects in object-oriented source code. Finally, this thesis proposes several novel aspect-oriented code smells. We validate the refactorings through an illustrative refactoring process.Idealmente, as ferramentas de engenharia de programas suportariam uma estrita separação de facetas, possibilitando a colocação de cada faceta na sua própria unidade modular. Infelizmente, as actuais ferramentas e linguagens – incluindo as que suportam o paradigma da orientação ao objecto – não conseguem obter uma completa e efectiva separação de todas as facetas. Daí resultam fenómenos indesejáveis tais como a dispersão e emaranhado de texto fonte. A programação orientada ao aspecto é um novo paradigma da programação capaz de modularizar facetas transversais. A orientação ao aspecto complementa os paradigmas existentes, incluindo a orientação ao objecto, com mecanismos que providenciam uma separação de facetas mais completa. A refabricação de programas é uma técnica para reestruturar o texto fonte de um programa no sentido de melhorar a concepção e estilo subjacentes, mantendo o seu comportamento externamente observável. “Maus cheiros” no texto fonte ajudam a detectar estruturas e concepções inadequadas, que são então gradualmente removidos através de processos de refabricação. Existe a perspectiva da orientação ao aspecto ter uma aceitação generalizada no futuro próximo. Coloca-se a questão de como lidar com uma grande base instalada de texto fonte orientado ao objecto legado quando tal acontecer. A compatibilidade retroactiva de AspectJ em relação a Java possibilita a refabricação das aplicações Java existentes de modo a tomarem partido dos conceitos e mecanismos dos aspectos. Porém, isto tem como pressuposto uma ideia clara de bom estilo para o texto fonte orientado ao aspecto, algo que actualmente não existe duma maneira desenvolvida e matura. Esta tese contribui para a caracterização de um novo estilo, apropriado à orientação ao aspecto. Para esse efeito, esta tese documenta uma colecção de refabricações originais através das quais facetas transversais existentes em texto legado orientado ao objecto são extraídas para aspectos, e a posterior reestruturação dos aspectos assim obtidos pode ser realizada. Esta tese apresenta também uma reapreciação dos maus cheiros orientados ao objecto tradicionais no sentido de poderem ser usados na detecção de aspectos latentes no texto fonte orientado ao objecto. Por fim, esta tese propõe diversos maus cheiros originais, orientados ao aspecto. As refabricações são validadas por meio de um processo de refabricação ilustrativo.Programa de Desenvolvimento Educativo para Portugal III (PRODEP III) - (Medida 5 - Acção 5.3 - Eixo 3 - Formação Avançada de Docentes do Ensino Superior).Portable Parallel Computing based on Virtual Machines (PPC-VM) - (PO-SI/CHS/47158/2002).Fundação Luso Americana para o Desenvolvimento (FLAD)

Design of new algorithms for gene network reconstruction applied to in silico modeling of biomedical data

Programa de Doctorado en Biotecnología, Ingeniería y Tecnología QuímicaLínea de Investigación: Ingeniería, Ciencia de Datos y BioinformáticaClave Programa: DBICódigo Línea: 111The root causes of disease are still poorly understood. The success of current therapies is limited because persistent diseases are frequently treated based on their symptoms rather than the underlying cause of the disease. Therefore, biomedical research is experiencing a technology-driven shift to data-driven holistic approaches to better characterize the molecular mechanisms causing disease. Using omics data as an input, emerging disciplines like network biology attempt to model the relationships between biomolecules. To this effect, gene co- expression networks arise as a promising tool for deciphering the relationships between genes in large transcriptomic datasets. However, because of their low specificity and high false positive rate, they demonstrate a limited capacity to retrieve the disrupted mechanisms that lead to disease onset, progression, and maintenance. Within the context of statistical modeling, we dove deeper into the reconstruction of gene co-expression networks with the specific goal of discovering disease-specific features directly from expression data. Using ensemble techniques, which combine the results of various metrics, we were able to more precisely capture biologically significant relationships between genes. We were able to find de novo potential disease-specific features with the help of prior biological knowledge and the development of new network inference techniques. Through our different approaches, we analyzed large gene sets across multiple samples and used gene expression as a surrogate marker for the inherent biological processes, reconstructing robust gene co-expression networks that are simple to explore. By mining disease-specific gene co-expression networks we come up with a useful framework for identifying new omics-phenotype associations from conditional expression datasets.In this sense, understanding diseases from the perspective of biological network perturbations will improve personalized medicine, impacting rational biomarker discovery, patient stratification and drug design, and ultimately leading to more targeted therapies.Universidad Pablo de Olavide de Sevilla. Departamento de Deporte e Informátic