This thesis analyzes major microarray repositories and presents a metadata framework both to address the current issues and to promote the main operations such as knowledge discovery, sharing, integration, and exchange. The proposed framework is demonstrated in a case study on real data and can be used for other high throughput repositories in biomedical domain. Not only the number of microarray experimentation increases, but also the size and complexity of the results rise in response to biomedical inquiries. And, experiment results are significant when examined in a batch and placed in a biological context. There have been standardization initiatives on content, object model, exchange format, and ontology. However, they have proprietary information space. There are backlogs and the data cannot be exchanged among the repositories. There is a need for a format and data management standard at present.iv v We introduced a metadata framework to include metadata card and semantic nets to make the experiment results visible, understandable and usable. They are encoded in standard syntax encoding schemes and represented in XML/RDF. They can be integrated with other metadata cards, semantic nets and can be queried. They can be exchanged and shared. We demonstrated the performance and potential benefits with a case study on a microarray repository. This study does not replace any product on repositories. A metadata framework is required to manage such huge data. We state that the backlogs can be reduced, complex knowledge discovery queries and exchange of information can become possible with this metadata framework.

The topic of this doctoral thesis is the potential near field immobilization of the radionuclide 79Se after intrusion of groundwater into a spent nuclear fuel canister in a repository. 79Se is a non naturally occurring long lived selenium isotope formed as a result of fission in nuclear fuel. Given the long half life (~3 x 105 y) and that the oxyanions of selenium are expected to be highly mobile and potentially difficult toimmobilize the isotope is of interest for the long term safety assessment of high level waste repositories. In this work the near field has been limited to the study of processes at or near the UO2 surface of (simulated) spent nuclear fuel and to processes occurring at or near the surface of iron (canister material) corroding under anoxic conditions. Selenite (HSeO32-) was found to adsorb onto palladium (simulated noble metal inclusion in spent nuclear fuel). Under hydrogen atmosphere selenite was reduced to elemental selenium with a rate constant of ~2 x 10-9 m s-1 (with respect to the Pd surface, 24 bar H2) forming colloidal particles. The rate constant of selenite reduction was increased by about two orders of magnitude to ~2.5 x 10-7 m s-1 (with respect to the Pd surface, 10 bar H2) for a UO2 surface doped with Pd particles, indicating that UO2 is an efficient co-catalyst to Pd. Selenate (SeO42-) was neither adsorbed nor reduced in the presence of Pd, UO2 and hydrogen. In the iron corrosion studies selenate was found to become reduced to predominantly elemental Se in the presence of a pristine iron surface. Iron covered by a corrosion layer of magnetite did however appear inert with respect to selenate whereas selenite was reduced. The reduction of dissolved uranyl into UO2 by the corroding iron surfaces was found to significantly increase the removal rate of selenite as well as selenate. The uranyl was found to transiently transform the outer iron oxide layers on the iron, forming a reactive mixed Fe(II)/Fe(III) oxyhydroxide (Green rust). Exchanging the solution and increasing the carbonate content (from 2 mM to 20 mM NaHCO3) only resulted in a minor, transient remobilization of uranium. Addition of H2O2 did however result in a significant release of uranium as well as selenium from the iron oxide surfaces. An irradiation experiment was also performed confirming the one electron reduction barrier of selenate as an important factor in systems where selenate reduction would be thermodynamically favorable. / QC 20101208

En el siglo pasado se ha desarrollado una nueva energía: la nuclear. Su aplicación comprende tanto el campo militar como el campo civil. Unos de los aspectos más interesantes es el uso de esta energía para la producción de electricidad de uso civil. El combustible nuclear es de larga duración: unas barras de uranio pueden llegar a producir energía eléctrica durante una década aproximadamente. Sin embargo, a mediados del siglo pasado se planteó el problema de los residuos nucleares. Este problema es muy complejo por que, aunque la duración del combustible sea de una década, el periodo de decaimiento es del orden de siglos. Esta tesis quiere aportar su granito de arena a esta nueva rama de la ciencia nuclear, estudiando algunos aspectos del comportamiento geotécnico de los agregados de sal, para su uso como material de relleno en los depósitos definitivos de los residuos nucleares de mayor peligrosidad.La regla fundamental de diseño de dichos depósitos es que su función debe desarrollarse sin la ayuda del hombre o de máquinas y que la misma naturaleza tiene que ser quien proteja al hombre del riesgo de radiaciones durante el transcurso de los siglos. Parece que al día de hoy la solución mundialmente aceptada es la de un depósito profundo en formaciones rocosas, a veces utilizando antiguas minas, incluso de sal. Se prevé que entre esta década y la próxima entrarán en funcionamiento varios de estos depósitos en los países en que la investigación en este área está más avanzada.En Europa se está haciendo un esfuerzo común, bajo supervisión de la Unión Europea y por medio de proyectos de investigación, para estudiar el funcionamiento del almacenamiento y la difusión de los resultados de esos estudios entre los miembros de la Unión Europea, a fin de dar el mayor provecho a las diferentes investigaciones que en la actualidad se están desarrollando en todos los centros de investigación de Europa.Esta tesis trata sobre el comportamiento termo hidráulico de los agregados de sal debido a las altas temperaturas que el decaimiento de los residuos nucleares produce. Este fenómeno crea unos efectos en los materiales de relleno y en la formación de base de alrededor del deposito.La tesis tiene un desarrollo básicamente experimental. En el laboratorio se realizaron fundamentalmente dos ensayos; el primero permitió determinar la curva de retención de los agregados de sal altamente compactados. Para ello se utilizó la técnica de traslación de ejes para aplicar la succión matricial y se construyó una placa de succión apta a los materiales salinos para la realización de estos ensayos.Este ensayo permitió determinar el comportamiento de una propiedad básica de los materiales salinos no saturados, sus resultados pudieron aplicarse al resto de los trabajos que se realizaron con posterioridad en esta tesis.El objeto del segundo ensayo de laboratorio fue reproducir los fenómenos de variación de porosidad debidos a la presencia de una diferencia de temperatura en las extremidades de la muestra. Dicho ensayo tiene una importancia fundamental para los almacenamientos profundos, porque los residuos radiactivos serán una fuente de calor durante varios siglos y la presencia de elevadas temperaturas induce fenómenos de flujo y transporte en el contacto con los contenedores de carburante nuclear agotado. Además, en el caso de los agregados de sal, a estos fenómenos cabe añadir el intercambio de sal entre la fase sólida y la líquida (precipitación /disolución).Para desarrollar estas pruebas de laboratorio, se dedicó una parte importante de la investigación al desarrollo y comprobación del equipo de ensayo, siendo éste poco convencional y completamente novedoso. Este último ensayo, en su segunda fase, fue convalidado mediante un modelo numérico (CODE BRIGHT). Los resultados del modelo numérico han permitido confirmar todo cuanto se determinó en la fase experimental y la importancia de la succión matricial en estos fenómenos.

Web application design is a broad term that refers to any aspect of designing a Web application, including designing Web interfaces to data. There are a number of commercial software tools available that employ various techniques for implementing Web access to databases. However, these techniques apply only to portions of Web application implementation and lack a common design paradigm. We believe that defining an approach to designing and implementing Web applications based on views, frameworks, and patterns allows us to extend an object-oriented design representation and develop reusable and extensible design solutions for a class of Web applications in which the concerns are separated. The major contribution of this thesis is the development of a new approach to designing Web applications, producing the following visible contributions: a model for Web applications based upon a separation of concerns using views; a framework for system elements so that object-oriented design patterns can be used to build the application; a reusable design approach so that many Web applications can be built around the same framework; a coherent and organized framework representation using extended UML; and an implementation approach that can be implemented on a number of different platforms using a range of software and tools. In support of this solution, this thesis shows the design and implementation of a proof-of-concept Web application using this design technique. We believe that the approach to Web application design promoted in this thesis has proven itself useful in a practical way for the case studies discussed herein and points the way to a wider range of design and implementation possibilities.

We report on initial research on the concurrency control issue of compiled database applications. Such applications have a repository style of architecture in which a collection of software modules operate on a common database in terms of a set of predefined transaction types, an architectural view that is useful for the deployment of database technology to embedded control programs. We focus on decoupling concurrency control from any functionality relating to recovery. Such decoupling facilitates the compile-time query optimization. <br /><br /> Because it is the possibility of transaction aborts for deadlock resolution that makes the recovery subsystem necessary, we choose the deadlock-free tree locking (TL) scheme for our purpose. With the knowledge of transaction workload, efficacious lock trees for runtime control can be determined at compile-time. We have designed compile-time algorithms to generate the lock tree and other relevant data structures, and runtime locking/unlocking algorithms based on such structures. We have further explored how to insert the lock steps into the transaction types at compile time. <br /><br /> To conduct our simulation experiments to evaluate the performance of TL, we have designed two workloads. The first one is from the OLTP benchmark TPC-C. The second is from the open-source operating system MINIX. Our experimental results show TL produces better throughput than the traditional two-phase locking (2PL) when the transactions are write-only; and for main-memory data, TL performs comparably to 2PL even in workloads with many reads.

Web application design is a broad term that refers to any aspect of designing a Web application, including designing Web interfaces to data. There are a number of commercial software tools available that employ various techniques for implementing Web access to databases. However, these techniques apply only to portions of Web application implementation and lack a common design paradigm. We believe that defining an approach to designing and implementing Web applications based on views, frameworks, and patterns allows us to extend an object-oriented design representation and develop reusable and extensible design solutions for a class of Web applications in which the concerns are separated. The major contribution of this thesis is the development of a new approach to designing Web applications, producing the following visible contributions: a model for Web applications based upon a separation of concerns using views; a framework for system elements so that object-oriented design patterns can be used to build the application; a reusable design approach so that many Web applications can be built around the same framework; a coherent and organized framework representation using extended UML; and an implementation approach that can be implemented on a number of different platforms using a range of software and tools. In support of this solution, this thesis shows the design and implementation of a proof-of-concept Web application using this design technique. We believe that the approach to Web application design promoted in this thesis has proven itself useful in a practical way for the case studies discussed herein and points the way to a wider range of design and implementation possibilities.

As the requirements for software systems increase, their size, complexity and functionality consequently increases as well. This has a direct impact on the complexity of numerous artifacts related to the system such as specification, design, implementation and, testing models. Furthermore, as the software market becomes more and more competitive, the need for software products that are of high quality and require the least monetary, time and human resources for their development and maintenance becomes evident. Therefore, it is important that project managers and software engineers are given the necessary tools to obtain a more holistic and accurate perspective of the status of their projects in order to early identify potential risks, flaws, and quality issues that may arise during each stage of the software project life cycle. In this respect, practitioners and academics alike have recognized the significance of investigating new methods for supporting software management operations with respect to large software projects. The main target of this M.A.Sc. thesis is the design of a framework in terms of, first, a reference architecture for mining and analyzing of software project data repositories according to specific objectives and analytic knowledge, second, the techniques to model such analytic knowledge and, third, a reasoning methodology for verifying or denying hypotheses related to analysis objectives. Such a framework could assist project managers, team leaders and development teams towards more accurate prediction of project traits such as quality analysis, risk assessment, cost estimation and progress evaluation. More specifically, the framework utilizes goal models to specify analysis objectives as well as, possible ways by which these objectives can be achieved. Examples of such analysis objectives for a project could be to yield, high code quality, achieve low production cost or, cope with tight delivery deadlines. Such goal models are consequently transformed into collections of Markov Logic Network rules which are then applied to the repository data in order to verify or deny with a degree of probability, whether the particular project objectives can be met as the project evolves. The proposed framework has been applied, as a proof of concept, on a repository pertaining to three industrial projects with more that one hundred development tasks.

A Content Management System (CMS) is a software application for creating, publishing, editing and managing content. The future step in content management system development is building intelligence over existing content resources that are heterogeneous in nature. Intelligence collected at the knowledge base can later on be used for executing semantic queries. Expressing the relations among content resources with ontological formalisms is therefore the key to implementing such semantic features. In this work, a methodology for the semantic lifting of JSR-170 compliant content repositories to ontologies is devised. The fact that in the worst case JSR-170 enforces no particular structural restrictions on the content model poses a technical challenge both for the initial build-up and further synchronization of the knowledge base. To address this problem, some recurring structural patterns in JSR-170 compliant content repositories are exploited. The value of the ontology extraction framework is assessed through a semantic search mechanism that is built on top of the extracted ontologies. The work in this thesis is complementary to the &ldquo / Interactive Knowledge Stack for small to medium CMS/KMS providers (IKS)&rdquo / project funded by the EC (FP7-ICT-2007-3).

<p>The increasing complexity of Information Systems (IS) calls for IS development methods to be adapted to the specific situations of the projects at hand. Method engineering is important because it focus on the creation of new methods that can be used in the system development process with the aim of constructing new information systems. The size and complexity of projects for developing information systems are becoming larger and more complicated. Therefore, development methods turn out to be one of the most significant key factors to achieve great success of development projects.</p><p>The discipline of Situational Method Engineering (SME) focuses on the creation of new project specific methods. SME is a reuse strategy to assemble reusable method fragments or method chunks originating from different methods. New methods can be constructed from a method repository by selecting the chunks that are the most appropriate to a given situation. Thus, method chunks are the basic building blocks for constructing methods in a modular way.</p><p>This dissertation have identified, analyzed and categorized a set of interoperability problems for the content of a method chunk repository. These problems have been represented as a set of patterns. The patterns will facilitate the understanding of specific interoperability problems that belong to a specific method chunk. If we are aware of the different interoperability problems that exist it is more likely that we can use a method chunk successfully within the context of SME.</p>

<p>For knowledge intense companies the knowledge and skills of its employees are much more valuable than any physical assets. To share knowledge between its employees, some companies launch knowledge sharing initiatives which aims to spread best practices and increase the expertise of the employees. These initiatives are often supported by technical systems, repositories, which store the information that is to be shared. This report discusses how the value of such a repository, a Wiki containing reference cases of SOA projects at IBM Nordic, can be increased by using processes that aims to better connect it to the organization.</p><p>To do this, seven employees at IBM Nordic were interviewed. Four of them were sales people, the main user group of the Wiki. Two were employees at the SOA Acceleration Team, the group responsible for the Wiki. The last interviewee works at Learning and Knowledge, IBM’s internal department for organization-wide knowledge management and education. The answers were analyzed using a framework created using academic theory. This framework consists of four different areas of requirements for the processes connecting the Wiki to the organization. The analysis showed that for IBM the most important area to manage is enablement followed by governance, motivation and finally content.</p><p>The report is concluded with recommendations for five processes to connect the Wiki to the organization. The process Internal selling aims to inform the sales people about the existence of the Wiki and how they are to use it. Ensure search engine compatibility makes sure that the sales people are able to find the contents of the Wiki via the intranet based search engines. The process for adding a new case description ensures that new case descriptions which are added to the Wiki is consistent and contains the right kind of information. By validating the case information that is added to the Wiki the acceleration team verifies that the information is correct, increasing its credibility. In the last process, ensure information congruence, the members of the acceleration team updates the guidelines on what information to collect and the information in the Wiki as the information need of the sales people changes. This is done on a regular basis and ensures that the information that is collected and stored is actually useful.</p>