Flexible virtual learning environments: a schema-driven approach using sematic web concepts

Flexible e-Iearning refers to an intelligent educational mechanism that focuses on simulating and improving traditional education as far as possible on the Web by integrating various electronic approaches, technologies, and equipment. This mechanism aims to promote the personalized development and management of e-learning Web services and applications. The main value of this method is that it provides high-powered individualization in pedagogy for students and staff.Here, the thesis mainly studied three problems in meeting the practical requirements of users in education. The first question is how a range of teaching styles (e.g. command and guided discovery) can be supported. The second one is how varieties of instructional processes can be authored. The third question is how these processes can be controlled by learners and educators in terms of their personalized needs during the execution of instruction.In this research, through investigating the existing e-Iearning approaches and technologies, the main technical problems of current virtual learning environments (VLEs) were analyzed. Next, by using the Semantic Web concepts as well as relevant standards, a schema-driven approach was created. This method can support users' individualized operations in the Web-based education. Then, a flexible e-learning system based on the approach was designed and implemented to map a range of extensive didactic paradigms. Finally, a case study was completed to evaluate the research results. The main findings of the assessment were that the flexible VLE implemented a range of teaching styles and the personalized creation and control of educational processes

A core ontological model for semantic sensor web infrastructures

Semantic Sensor Web infrastructures use ontology-based models to represent the data that they manage; however, up to now, these ontological models do not allow representing all the characteristics of distributed, heterogeneous, and web-accessible sensor data. This paper describes a core ontological model for Semantic Sensor Web infrastructures that covers these characteristics and that has been built with a focus on reusability. This ontological model is composed of different modules that deal, on the one hand, with infrastructure data and, on the other hand, with data from a specific domain, that is, the coastal flood emergency planning domain. The paper also presents a set of guidelines, followed during the ontological model development, to satisfy a common set of requirements related to modelling domain-specific features of interest and properties. In addition, the paper includes the results obtained after an exhaustive evaluation of the developed ontologies along different aspects (i.e., vocabulary, syntax, structure, semantics, representation, and context)

Epigenetics of complex traits and diseases

Thousands of genetic and epigenetic variants have been identified for many common diseases including cancer through genome-wide association studies (GWAS) and epigenome-wide association studies (EWAS). To advance the complex interpretation of both GWAS and EWAS results, I developed new software tools (FORGE2 and eFORGE) for the analysis and interpretation of GWAS and EWAS data, respectively. Both tools determine the cell type-specific regulatory component of a set of target regions (either GWAS-identified genetic variants or EWAS-identified differentially methylated positions). This is achieved by detecting enrichment of overlap with histone mark peaks or DNase I hypersensitive sites across hundreds of tissues, primary cell types, and cell lines from the ENCODE, Roadmap Epigenomics, and BLUEPRINT projects. Application of both tools to publicly available datasets identified novel disease-relevant cell types for many common diseases, a stem cell-like signature in cancer EWAS, and also demonstrated the ability to detect cell-composition effects for EWAS performed on heterogeneous tissues. To complement these bioinformatics efforts and validate selected variants predicted by FORGE2, eFORGE and additional analyses, I performed conformation capture using 4C-seq to fine-map the 3D context of the genomic regions involved, uncovering novel interactions for autoimmunity-associated variants and IKZF3

Final FLaReNet deliverable: Language Resources for the Future - The Future of Language Resources

Language Technologies (LT), together with their backbone, Language Resources (LR), provide an essential support to the challenge of Multilingualism and ICT of the future. The main task of language technologies is to bridge language barriers and to help creating a new environment where information flows smoothly across frontiers and languages, no matter the country, and the language, of origin. To achieve this goal, all players involved need to act as a community able to join forces on a set of shared priorities. However, until now the field of Language Resources and Technology has long suffered from an excess of individuality and fragmentation, with a lack of coherence concerning the priorities for the field, the direction to move, not to mention a common timeframe. The context encountered by the FLaReNet project was thus represented by an active field needing a coherence that can only be given by sharing common priorities and endeavours. FLaReNet has contributed to the creation of this coherence by gathering a wide community of experts and making them participate in the definition of an exhaustive set of recommendations

Usage Analysis & Demonstrators - Version 2.0

This second version of the "Usage Analysis and Demonstrators " document mainly presents four case studies done during the second part of the SCOrWare project: ● (Task 3.1) Component and service-oriented architecture in the Scientific Software field (improvements of works done during the first year) ● (Task 3.2) SCA as a SOA design methodology in the domain of CDE (Collaborative Development Environment). Following the withdraw of one of the partners (eXo Platform, provider of an open-source portal solution) during the first year, some changes have been decided during the second part of the project and an alternative demonstrator has been designed. ● (Task 3.3) How SCA contributes to reusing and enriching software components. Following the first year project's review, this scenario has been reinforced, and is the major demonstrator for the SCOrWare platform in the field of enterprise business applications. ● (Task 3.5) Using the SCOrWare platform and a component-oriented architecture in the context of a network monitoring system. A new partner (Thales Communications, in collaboration with Open Wide and EBM Websourcing) has joined the SCOrWare consortium during the second part of the project, following the withdraw of Amadeus

Doctor of Philosophy

dissertationThe MAKER genome annotation and curation software tool was developed in response to increased demand for genome annotation services, secondary to decreased genome sequencing costs. MAKER currently has over 1000 registered users throughout the world. This wide adoption of MAKER has uncovered the need for additional functionalities. Here I addressed moving MAKER into the domain of plant annotation, expanding MAKER to include new methods of gene and noncoding RNA annotation, and improving usability of MAKER through documentation and community outreach. To move MAKER into the plant annotation domain, I benchmarked MAKER on the well-annotated Arabidopsis thaliana genome. MAKER performs well on the Arabidopsis genome in de novo genome annotation and was able to improve the current TAIR10 gene models by incorporating mRNA-seq data not available during the original annotation efforts. In addition to this benchmarking, I annotated the genome of the sacred lotus Nelumbo Nucifera. I enabled noncoding RNA annotation in MAKER by adding the ability for MAKER to run and process the outputs of tRNAscan-SE and snoscan. These functionalities were tested on the Arabidopsis genome and used MAKER to annotate tRNAs and snoRNAs in Zea mays. The resulting version of MAKER was named MAKER-P. I added the functionality of a combiner by adding EVidence Modeler to the MAKER code base. iv As the number of MAKER users has grown, so have the help requests sent to the MAKER developers list. Motivated by the belief that improving the MAKER documentation would obviate the need for many of these requests, I created a media wiki that was linked to the MAKER download page, and the MAKER developers list was made searchable. Additionally I have written a unit on genome annotation using MAKER for Current Protocols in Bioinformatics. In response to these efforts I have seen a corresponding decrease in help requests, even though the number of registered MAKER users continues to increase. Taken together these products and activities have moved MAKER into the domain of plant annotation, expanded MAKER to include new methods of gene and noncoding RNA annotation, and improved the usability of MAKER through documentation and community outreach

Ontology-Driven Semantic Annotations for Multiple Engineering Viewpoints in Computer Aided Design

Engineering design involves a series of activities to handle data, including capturing and storing data, retrieval and manipulation of data. This also applies throughout the entire product lifecycle (PLC). Unfortunately, a closed loop of knowledge and information management system has not been implemented for the PLC. As part of product lifecycle management (PLM) approaches, computer-aided design (CAD) systems are extensively used from embodiment and detail design stages in mechanical engineering. However, current CAD systems lack the ability to handle semantically-rich information, thus to represent, manage and use knowledge among multidisciplinary engineers, and to integrate various tools/services with distributed data and knowledge. To address these challenges, a general-purpose semantic annotation approach based on CAD systems in the mechanical engineering domain is proposed, which contributes to knowledge management and reuse, data interoperability and tool integration. In present-day PLM systems, annotation approaches are currently embedded in software applications and use diverse data and anchor representations, making them static, inflexible and difficult to incorporate with external systems. This research will argue that it is possible to take a generalised approach to annotation with formal annotation content structures and anchoring mechanisms described using general-purpose ontologies. In this way viewpoint-oriented annotation may readily be captured, represented and incorporated into PLM systems together with existing annotations in a common framework, and the knowledge collected or generated from multiple engineering viewpoints may be reasoned with to derive additional knowledge to enable downstream processes. Therefore, knowledge can be propagated and evolved through the PLC. Within this framework, a knowledge modelling methodology has also been proposed for developing knowledge models in various situations. In addition, a prototype system has been designed and developed in order to evaluate the core contributions of this proposed concept. According to an evaluation plan, cost estimation and finite element analysis as case studies have been used to validate the usefulness, feasibility and generality of the proposed framework. Discussion has been carried out based on this evaluation. As a conclusion, the presented research work has met the original aim and objectives, and can be improved further. At the end, some research directions have been suggested.EThOS - Electronic Theses Online ServiceGBUnited Kingdo