Improving discovery in the life sciences using semantic Web technologies and linked data: design principles for life sciences knowledge organization systems

Dissertation presented to obtain the Ph.D degree in Bioinformatics

Development of process control strategies exploiting knowledge from systems biology: application to MDCK suspension cells

Madine Darby Canine Kidney (MDCK) cell lines have been extensively evaluated for their potential as host cells for influenza vaccine production. Recent studies allowed the cultivation of these cells in a fully defined medium and in suspension. However, reaching high cell densities in animal cell cultures still remains a challenge. To address this shortcoming, a combined methodology allied with knowledge from systems biology was reported to study the impact of the cell environment on the flux distribution. An optimization of the medium composition was proposed for both a batch and a continuous system in order to reach higher cell densities. To obtain insight into the metabolic activity of these cells, a detailed metabolic model previously developed by Wahl A. et. al was used. The experimental data of four cultivations of MDCK suspension cells, grown under different conditions and used in this work came from the Max Planck Institute, Magdeburg, Germany. Classical metabolic flux analysis (MFA) was used to estimate the intracellular flux distribution of each cultivation and then combined with partial least squares (PLS) method to establish a link between the estimated metabolic state and the cell environment. The validation of the MFA model was made and its consistency checked. The resulted PLS model explained almost 70% of the variance present in the flux distribution. The medium optimization for the continuous system and for the batch system resulted in higher biomass growth rates than the ones obtained experimentally, 0.034 h-1 and 0.030 h-1, respectively, thus reducing in almost 10 hours the duplication time. Additionally, the optimal medium obtained for the continuous system almost did not consider pyruvate. Overall the proposed methodology seems to be effective and both proposed medium optimizations seem to be promising to reach high cell densities.

A process-based control for evolvable production systems

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores

Hybrid systems biology: application to Escherichia coli

Dissertation presented to obtain a Master degree in Biotechnology

Semantic adaptability for the systems interoperability

In the current global and competitive business context, it is essential that enterprises adapt their knowledge resources in order to smoothly interact and collaborate with others. However, due to the existent multiculturalism of people and enterprises, there are different representation views of business processes or products, even inside a same domain. Consequently, one of the main problems found in the interoperability between enterprise systems and applications is related to semantics. The integration and sharing of enterprises knowledge to build a common lexicon, plays an important role to the semantic adaptability of the information systems. The author proposes a framework to support the development of systems to manage dynamic semantic adaptability resolution. It allows different organisations to participate in a common knowledge base building, letting at the same time maintain their own views of the domain, without compromising the integration between them. Thus, systems are able to be aware of new knowledge, and have the capacity to learn from it and to manage its semantic interoperability in a dynamic and adaptable way. The author endorses the vision that in the near future, the semantic adaptability skills of the enterprise systems will be the booster to enterprises collaboration and the appearance of new business opportunities.

Relational navigation and archiving of multimedia information for contemporary dance

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Reactive hybrid knowledge bases

Hybrid knowledge bases are knowledge bases that combine ontologies with non-monotonic rules, allowing to join the best of both open world ontologies and close world rules. Ontologies shape a good mechanism to share knowledge on theWeb that can be understood by both humans and machines, on the other hand rules can be used, e.g., to encode legal laws or to do a mapping between sources of information. Taking into account the dynamics present today on the Web, it is important for these hybrid knowledge bases to capture all these dynamics and thus adapt themselves. To achieve that, it is necessary to create mechanisms capable of monitoring the information flow present on theWeb. Up to today, there are no such mechanisms that allow for monitoring events and performing modifications of hybrid knowledge bases autonomously. The goal of this thesis is then to create a system that combine these hybrid knowledge bases with reactive rules, aiming to monitor events and perform actions over a knowledge base. To achieve this goal, a reactive system for the SemanticWeb is be developed in a logic-programming based approach accompanied with a language for heterogeneous rule base evolution having as its basis RIF Production Rule Dialect, which is a standard for exchanging rules over theWeb.

Transactions in dynamic reactive environments

Most of today’s systems, especially when related to the Web or to multi-agent systems, are not standalone or independent, but are part of a greater ecosystem, where they need to interact with other entities, react to complex changes in the environment, and act both over its own knowledge base and on the external environment itself. Moreover, these systems are clearly not static, but are constantly evolving due to the execution of self updates or external actions. Whenever actions and updates are possible, the need to ensure properties regarding the outcome of performing such actions emerges. Originally purposed in the context of databases, transactions solve this problem by guaranteeing atomicity, consistency, isolation and durability of a special set of actions. However, current transaction solutions fail to guarantee such properties in dynamic environments, since they cannot combine transaction execution with reactive features, or with the execution of actions over domains that the system does not completely control (thus making rolling back a non-viable proposition). In this thesis, we investigate what and how transaction properties can be ensured over these dynamic environments. To achieve this goal, we provide logic-based solutions, based on Transaction Logic, to precisely model and execute transactions in such environments, and where knowledge bases can be defined by arbitrary logic theories.

Gestão de Informação: Inteligência Artificial

A informação e a sua gestão é considerada nos nossos dias como o principal factor de sucesso ou insucesso para qualquer actividade económica ou social. O desenvolvimento de novas tecnologias força todos os agentes econcómicos a desenvolverem-se nestas áreas para conseguirem vantagens concorrenciais. Este trabalho visa fazer uma apresentação de uma “nova” área da ciência da computação a que se chamou Inteligência Artificial.

Intention recognition, commitment and their roles in the evolution of cooperation

Dissertação para obtenção do Grau de Doutor em Informática

People and object tracking for video annotation

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Directivas antecipadas de vida : modelo de aferição da sua aceitabilidade nas unidades de saúde em Portugal

RESUMO - As Directivas Antecipadas de Vida, são instruções escritas ou orais formuladas por uma pessoa competente relativamente à prestação ou suspensão de cuidados médicos numa eventual situação de doença geradora de incapacidade para decidir ou expressar a sua vontade (Neves et al., 2010). No presente estudo, o problema de investigação centra-se em saber de que forma a construção de um modelo de Directivas Antecipadas de Vida pode contribuir para uma melhor gestão nas unidades de saúde? Para a realização do presente projecto de investigação, foi efectuada uma pesquisa bibliográfica sobre os principais conceitos e estado actual do conhecimento, os quais contribuíram para a definição dos objectivos de investigação empírica:  Contribuir para a criação de um corpo de conhecimento no que diz respeito às Directivas Antecipadas de Vida com a elaboração de uma proposta de um modelo de aferição da sua aceitabilidade nas unidades de saúde em Portugal.  Identificar os diferentes intervenientes, e qual o seu papel na implementação do modelo proposto. No que se refere ao estudo das Directivas Antecipadas de Vida em Portugal, e em especial nas unidades de saúde, recorreu-se a uma metodologia exploratória e descritiva, para identificar as principais características e trabalhos desenvolvidos na área em investigação. A primeira conclusão reside nas características da própria sociedade, a qual não parece ainda estar suficientemente desperta para a problemática em estudo, não obstante se verificar a existência de iniciativas legislativas recentemente apresentadas. Esta constatação verifica-se igualmente ao nível das unidades prestadoras de cuidados de saúde.

Improvements in the geocoding process in organizational environments

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Video interaction using pen-based technology

Dissertação para obtenção do Grau de Doutor em Informática

Redes de Nova Geração: Uma Proposta para Cadastro em Sistemas de Informação Geográfica de Redes Fixas de Telecomunicações em Fibra Óptica

Dissertação apresentada para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Gestão do Território variante de Sistemas de Informação Geográfica e Detecção Remota