Software Visualization in 3D: Implementation, Evaluation, and Applicability

The focus of this thesis is on the implementation, the evaluation and the useful application of the third dimension in software visualization. Software engineering is characterized by a complex interplay of different stakeholders that produce and use several artifacts. Software visualization is used as one mean to address this increasing complexity. It provides role- and task-specific views of artifacts that contain information about structure, behavior, and evolution of a software system in its entirety. The main potential of the third dimension is the possibility to provide multiple views in one software visualization for all three aspects. However, empirical findings concerning the role of the third dimension in software visualization are rare. Furthermore, there are only few 3D software visualizations that provide multiple views of a software system including all three aspects. Finally, the current tool support lacks of generating easy integrateable, scalable, and platform independent 2D, 2.5D, and 3D software visualizations automatically. Hence, the objective is to develop a software visualization that represents all important structural entities and relations of a software system, that can display behavioral and evolutionary aspects of a software system as well, and that can be generated automatically. In order to achieve this objective the following research methods are applied. A literature study is conducted, a software visualization generator is conceptualized and prototypically implemented, a structured approach to plan and design controlled experiments in software visualization is developed, and a controlled experiment is designed and performed to investigate the role of the third dimension in software visualization. The main contributions are an overview of the state-of-the-art in 3D software visualization, a structured approach including a theoretical model to control influence factors during controlled experiments in software visualization, an Eclipse-based generator for producing automatically role- and task-specific 2D, 2.5D, and 3D software visualizations, the controlled experiment investigating the role of the third dimension in software visualization, and the recursive disk metaphor combining the findings with focus on the structure of software including useful applications of the third dimension regarding behavior and evolution

MACHS: Mitigating the Achilles Heel of the Cloud through High Availability and Performance-aware Solutions

Cloud computing is continuously growing as a business model for hosting information and communication technology applications. However, many concerns arise regarding the quality of service (QoS) offered by the cloud. One major challenge is the high availability (HA) of cloud-based applications. The key to achieving availability requirements is to develop an approach that is immune to cloud failures while minimizing the service level agreement (SLA) violations. To this end, this thesis addresses the HA of cloud-based applications from different perspectives. First, the thesis proposes a component’s HA-ware scheduler (CHASE) to manage the deployments of carrier-grade cloud applications while maximizing their HA and satisfying the QoS requirements. Second, a Stochastic Petri Net (SPN) model is proposed to capture the stochastic characteristics of cloud services and quantify the expected availability offered by an application deployment. The SPN model is then associated with an extensible policy-driven cloud scoring system that integrates other cloud challenges (i.e. green and cost concerns) with HA objectives. The proposed HA-aware solutions are extended to include a live virtual machine migration model that provides a trade-off between the migration time and the downtime while maintaining HA objective. Furthermore, the thesis proposes a generic input template for cloud simulators, GITS, to facilitate the creation of cloud scenarios while ensuring reusability, simplicity, and portability. Finally, an availability-aware CloudSim extension, ACE, is proposed. ACE extends CloudSim simulator with failure injection, computational paths, repair, failover, load balancing, and other availability-based modules

A Novel Virtual Product Modelling Framework for Design Automation in a Knowledge-Based Engineering Environment

Computer Aided Design (CAD) has been widely used for product modelling in the industry, where multiple issues arise, such as lack of product data representation and capturing and reusing the existing design knowledge in the modelling process. Existing CAD systems only provide geometric data within the CAD models and require users to have knowledge of the product to judge the correctness of the modelling process. Knowledge-Based Engineering (KBE) has been introduced to assist product design with the capabilities of knowledge capturing and reusing. However, there is always a “black box” problem in understanding the existing KBE applications, and the substantiation steps for the implementation of KBE frameworks are still limited. To address this, the author proposed and implemented a Virtual Product Modelling (VPM) framework that helps capture and reuse existing product information to enhance the modelling process for design automation. This framework was built as a knowledge-based product modelling environment using a gaming engine. It was further evaluated through three use cases, where the proposed framework was applied to simple parts with primitive geometric features, a hex bolt, and a wheel assembly. The results of the use case evaluation indicate that this framework satisfies all the identified measurement parameters and achieves the aim of the research. This research enhances the product modelling process with the capabilities of generative representation, knowledge capturing and reusing. It provides design engineers with the knowledge reasoning capability when they are making changes to the product model and, therefore, saves time and prevents engineers from making mistakes. This research also presents a KBE implementation framework with detailed substantiation steps, where the knowledge is structured and reusable within the product model. Further, the findings of this research have shown the potential of the developed VPM framework in aspects such as standard development in product modelling, extending to non-engineers and integration with VR/AR visualisation techniques

An object query language for multimedia federations

The Fischlar system provides a large centralised repository of multimedia files. As expansion is difficult in centralised systems and as different user groups have a requirement to define their own schemas, the EGTV (Efficient Global Transactions for Video) project was established to examine how the distribution of this database could be managed. The federated database approach is advocated where global schema is designed in a top-down approach, while all multimedia and textual data is stored in object-oriented (O-O) and object-relational (0-R) compliant databases. This thesis investigates queries and updates on large multimedia collections organised in the database federation. The goal of this research is to provide a generic query language capable of interrogating global and local multimedia database schemas. Therefore, a new query language EQL is defined to facilitate the querying of object-oriented and objectrelational database schemas in a database and platform independent manner, and acts as a canonical language for database federations. A new canonical language was required as the existing query language standards (SQL: 1999 and OQL) axe generally incompatible and translation between them is not trivial. EQL is supported with a formally defined object algebra and specified semantics for query evaluation. The ability to capture and store metadata of multiple database schemas is essential when constructing and querying a federated schema. Therefore we also present a new platform independent metamodel for specifying multimedia schemas stored in both object-oriented and object-relational databases. This metadata information is later used for the construction of a global schemas, and during the evaluation of local and global queries. Another important feature of any federated system is the ability to unambiguously define database schemas. The schema definition language for an EGTV database federation must be capable of specifying both object-oriented and object-relational schemas in the database independent format. As XML represents a standard for encoding and distributing data across various platforms, a language based upon XML has been developed as a part of our research. The ODLx (Object Definition Language XML) language specifies a set of XMLbased structures for defining complex database schemas capable of representing different multimedia types. The language is fully integrated with the EGTV metamodel through which ODLx schemas can be mapped to 0-0 and 0-R databases

CReATIVE-B Deliverable D3.1: Comparison of technical basis of biodiversity e-infrastructures

Deliverable D3.1, prepared on the basis of available information at the time of writing, is the output of CReATIVE-B task T3.1, which aims to “Compare the technical basis of e-infrastructures for biodiversity research”. It provides a synopsis comparison of the technical approaches of the e-infrastructures analysed within the scope of the project and elaborates the interoperability analysis by defining it and making a quantitative comparison of the technical facts gathered thus far. It reflects as accurately as possible the technical findings, structured along dimensions of interoperability that match the functional areas and layers of the research infrastructures being analysed. Deliverable D3.1 aims at shedding light on existing similarities and differences between participating research infrastructures thus forming a solid information and knowledge basis for future interoperability guidelines developments in D3.2 and D3.3

Aplicação de técnicas de Clustering ao contexto da Tomada de Decisão em Grupo

Nowadays, decisions made by executives and managers are primarily made in a group. Therefore, group decision-making is a process where a group of people called participants work together to analyze a set of variables, considering and evaluating a set of alternatives to select one or more solutions. There are many problems associated with group decision-making, namely when the participants cannot meet for any reason, ranging from schedule incompatibility to being in different countries with different time zones. To support this process, Group Decision Support Systems (GDSS) evolved to what today we call web-based GDSS. In GDSS, argumentation is ideal since it makes it easier to use justifications and explanations in interactions between decision-makers so they can sustain their opinions. Aspect Based Sentiment Analysis (ABSA) is a subfield of Argument Mining closely related to Natural Language Processing. It intends to classify opinions at the aspect level and identify the elements of an opinion. Applying ABSA techniques to Group Decision Making Context results in the automatic identification of alternatives and criteria, for example. This automatic identification is essential to reduce the time decision-makers take to step themselves up on Group Decision Support Systems and offer them various insights and knowledge on the discussion they are participants. One of these insights can be arguments getting used by the decision-makers about an alternative. Therefore, this dissertation proposes a methodology that uses an unsupervised technique, Clustering, and aims to segment the participants of a discussion based on arguments used so it can produce knowledge from the current information in the GDSS. This methodology can be hosted in a web service that follows a micro-service architecture and utilizes Data Preprocessing and Intra-sentence Segmentation in addition to Clustering to achieve the objectives of the dissertation. Word Embedding is needed when we apply clustering techniques to natural language text to transform the natural language text into vectors usable by the clustering techniques. In addition to Word Embedding, Dimensionality Reduction techniques were tested to improve the results. Maintaining the same Preprocessing steps and varying the chosen Clustering techniques, Word Embedders, and Dimensionality Reduction techniques came up with the best approach. This approach consisted of the KMeans++ clustering technique, using SBERT as the word embedder with UMAP dimensionality reduction, reducing the number of dimensions to 2. This experiment achieved a Silhouette Score of 0.63 with 8 clusters on the baseball dataset, which wielded good cluster results based on their manual review and Wordclouds. The same approach obtained a Silhouette Score of 0.59 with 16 clusters on the car brand dataset, which we used as an approach validation dataset.Atualmente, as decisões tomadas por gestores e executivos são maioritariamente realizadas em grupo. Sendo assim, a tomada de decisão em grupo é um processo no qual um grupo de pessoas denominadas de participantes, atuam em conjunto, analisando um conjunto de variáveis, considerando e avaliando um conjunto de alternativas com o objetivo de selecionar uma ou mais soluções. Existem muitos problemas associados ao processo de tomada de decisão, principalmente quando os participantes não têm possibilidades de se reunirem (Exs.: Os participantes encontramse em diferentes locais, os países onde estão têm fusos horários diferentes, incompatibilidades de agenda, etc.). Para suportar este processo de tomada de decisão, os Sistemas de Apoio à Tomada de Decisão em Grupo (SADG) evoluíram para o que hoje se chamam de Sistemas de Apoio à Tomada de Decisão em Grupo baseados na Web. Num SADG, argumentação é ideal pois facilita a utilização de justificações e explicações nas interações entre decisores para que possam suster as suas opiniões. Aspect Based Sentiment Analysis (ABSA) é uma área de Argument Mining correlacionada com o Processamento de Linguagem Natural. Esta área pretende classificar opiniões ao nível do aspeto da frase e identificar os elementos de uma opinião. Aplicando técnicas de ABSA à Tomada de Decisão em Grupo resulta na identificação automática de alternativas e critérios por exemplo. Esta identificação automática é essencial para reduzir o tempo que os decisores gastam a customizarem-se no SADG e oferece aos mesmos conhecimento e entendimentos sobre a discussão ao qual participam. Um destes entendimentos pode ser os argumentos a serem usados pelos decisores sobre uma alternativa. Assim, esta dissertação propõe uma metodologia que utiliza uma técnica não-supervisionada, Clustering, com o objetivo de segmentar os participantes de uma discussão com base nos argumentos usados pelos mesmos de modo a produzir conhecimento com a informação atual no SADG. Esta metodologia pode ser colocada num serviço web que segue a arquitetura micro serviços e utiliza Preprocessamento de Dados e Segmentação Intra Frase em conjunto com o Clustering para atingir os objetivos desta dissertação. Word Embedding também é necessário para aplicar técnicas de Clustering a texto em linguagem natural para transformar o texto em vetores que possam ser usados pelas técnicas de Clustering. Também Técnicas de Redução de Dimensionalidade também foram testadas de modo a melhorar os resultados. Mantendo os passos de Preprocessamento e variando as técnicas de Clustering, Word Embedder e as técnicas de Redução de Dimensionalidade de modo a encontrar a melhor abordagem. Essa abordagem consiste na utilização da técnica de Clustering KMeans++ com o SBERT como Word Embedder e UMAP como a técnica de redução de dimensionalidade, reduzindo as dimensões iniciais para duas. Esta experiência obteve um Silhouette Score de 0.63 com 8 clusters no dataset de baseball, que resultou em bons resultados de cluster com base na sua revisão manual e visualização dos WordClouds. A mesma abordagem obteve um Silhouette Score de 0.59 com 16 clusters no dataset das marcas de carros, ao qual usamos esse dataset com validação de abordagem

Information management applied to bioinformatics

Bioinformatics, the discipline concerned with biological information management is essential in the post-genome era, where the complexity of data processing allows for contemporaneous multi level research including that at the genome level, transcriptome level, proteome level, the metabolome level, and the integration of these -omic studies towards gaining an understanding of biology at the systems level. This research is also having a major impact on disease research and drug discovery, particularly through pharmacogenomics studies. In this study innovative resources have been generated via the use of two case studies. One was of the Research & Development Genetics (RDG) department at AstraZeneca, Alderley Park and the other was of the Pharmacogenomics Group at the Sanger Institute in Cambridge UK. In the AstraZeneca case study senior scientists were interviewed using semi-structured interviews to determine information behaviour through the study scientific workflows. Document analysis was used to generate an understanding of the underpinning concepts and fonned one of the sources of context-dependent information on which the interview questions were based. The objectives of the Sanger Institute case study were slightly different as interviews were carried out with eight scientists together with the use of participation observation, to collect data to develop a database standard for one process of their Pharmacogenomics workflow. The results indicated that AstraZeneca would benefit through upgrading their data management solutions in the laboratory and by development of resources for the storage of data from larger scale projects such as whole genome scans. These studies will also generate very large amounts of data and the analysis of these will require more sophisticated statistical methods. At the Sanger Institute a minimum information standard was reported for the manual design of primers and included in a decision making tree developed for Polymerase Chain Reactions (PCRs). This tree also illustrates problems that can be encountered when designing primers along with procedures that can be taken to address such issues.EThOS - Electronic Theses Online ServiceGBUnited Kingdo