Reverse Engineering Heterogeneous Applications

Nowadays a large majority of software systems are built using various technologies that in turn rely on different languages (e.g. Java, XML, SQL etc.). We call such systems heterogeneous applications (HAs). By contrast, we call software systems that are written in one language homogeneous applications. In HAs the information regarding the structure and the behaviour of the system is spread across various components and languages and the interactions between different application elements could be hidden. In this context applying existing reverse engineering and quality assurance techniques developed for homogeneous applications is not enough. These techniques have been created to measure quality or provide information about one aspect of the system and they cannot grasp the complexity of HAs. In this dissertation we present our approach to support the analysis and evolution of HAs based on: (1) a unified first-class description of HAs and, (2) a meta-model that reifies the concept of horizontal and vertical dependencies between application elements at different levels of abstraction. We implemented our approach in two tools, MooseEE and Carrack. The first is an extension of the Moose platform for software and data analysis and contains our unified meta-model for HAs. The latter is an engine to infer derived dependencies that can support the analysis of associations among the heterogeneous elements composing HA. We validate our approach and tools by case studies on industrial and open-source JEAs which demonstrate how we can handle the complexity of such applications and how we can solve problems deriving from their heterogeneous nature

Discovering lesser known molecular players and mechanistic patterns in Alzheimer's disease using an integrative disease modelling approach

Convergence of exponentially advancing technologies is driving medical research with life changing discoveries. On the contrary, repeated failures of high-profile drugs to battle Alzheimer's disease (AD) has made it one of the least successful therapeutic area. This failure pattern has provoked researchers to grapple with their beliefs about Alzheimer's aetiology. Thus, growing realisation that Amyloid-β and tau are not 'the' but rather 'one of the' factors necessitates the reassessment of pre-existing data to add new perspectives. To enable a holistic view of the disease, integrative modelling approaches are emerging as a powerful technique. Combining data at different scales and modes could considerably increase the predictive power of the integrative model by filling biological knowledge gaps. However, the reliability of the derived hypotheses largely depends on the completeness, quality, consistency, and context-specificity of the data. Thus, there is a need for agile methods and approaches that efficiently interrogate and utilise existing public data. This thesis presents the development of novel approaches and methods that address intrinsic issues of data integration and analysis in AD research. It aims to prioritise lesser-known AD candidates using highly curated and precise knowledge derived from integrated data. Here much of the emphasis is put on quality, reliability, and context-specificity. This thesis work showcases the benefit of integrating well-curated and disease-specific heterogeneous data in a semantic web-based framework for mining actionable knowledge. Furthermore, it introduces to the challenges encountered while harvesting information from literature and transcriptomic resources. State-of-the-art text-mining methodology is developed to extract miRNAs and its regulatory role in diseases and genes from the biomedical literature. To enable meta-analysis of biologically related transcriptomic data, a highly-curated metadata database has been developed, which explicates annotations specific to human and animal models. Finally, to corroborate common mechanistic patterns — embedded with novel candidates — across large-scale AD transcriptomic data, a new approach to generate gene regulatory networks has been developed. The work presented here has demonstrated its capability in identifying testable mechanistic hypotheses containing previously unknown or emerging knowledge from public data in two major publicly funded projects for Alzheimer's, Parkinson's and Epilepsy diseases

Cognitive Buildings

Cognitive building is a pioneering topic envisioning the future of our built environment. The concept of "cognitive" provides a paradigm shift that steps from the static concept of the building as a container of human activities towards the modernist vision of "machine à habiter" of Le Corbusier, where the technological content adds the capability of learning from users' behavior and environmental variables to adapt itself to achieve major goals such as user comfort, energy-saving, flexible functionality, high durability, and good maintainability. The concept is based on digital frameworks and IoT networks towards the concept of a smart city