Web competitive intelligence methodology

Master’s Degree DissertationThe present dissertation covers academic concerns in disruptive change that causes value displacements in today’s competitive economic environment. To enhance survival capabilities organizations are increasing efforts in more untraditional business value assets such intellectual capital and competitive intelligence. Dynamic capabilities, a recent strategy theory states that companies have to develop adaptive capabilities to survive disruptive change and increase competitive advantage in incremental change phases. Taking advantage of the large amount of information in the World Wide Web it is propose a methodology to develop applications to gather, filter and analyze web data and turn it into usable intelligence (WeCIM). In order to enhance information search and management quality it is proposed the use of ontologies that allow computers to “understand” particular knowledge domains. Two case studies were conducted with satisfactory results. Two software prototypes were developed according to the proposed methodology. It is suggested that even a bigger step can be made. Not only the success of the methodology was proved but also common software architecture elements are present which suggests that a solid base can be design for different field applications based on web competitive intelligence tools

NEGOSEIO: framework for the sustainability of model-oriented enterprise interoperability

Dissertation to obtain the degree of Doctor of Philosophy in Electrical and Computer Engineering(Industrial Information Systems)This dissertation tackles the problematic of Enterprise Interoperability in the current globally connected world. The evolution of the Information and Communication Technologies has endorsed the establishment of fast, secure and robust data exchanges, promoting the development of networked solutions. This allowed the specialisation of enterprises (particularly SMEs) and favoured the development of complex and heterogeneous provider systems. Enterprises are abandoning their self-centrism and working together on the development of more complete solutions. Entire business solutions are built integrating several enterprises (e.g., in supply chains, enterprise nesting) towards a common objective. Additionally, technologies, platforms, trends, standards and regulations keep evolving and demanding enterprises compliance. This evolution needs to be continuous, and is naturally followed by a constant update of each networked enterprise’s interfaces, assets, methods and processes. This unstable environment of perpetual change is causing major concerns in both SMEs and customers as the current interoperability grounds are frail, easily leading to periods of downtime, where business is not possible. The pressure to restore interoperability rapidly often leads to patching and to the adoption of immature solutions, contributing to deteriorate even more the interoperable environment. This dissertation proposes the adoption of NEGOSEIO, a framework that tackles interoperability issues by developing strong model-based knowledge assets and promoting continuous improvement and adaptation for increasing the sustainability of interoperability on enterprise systems. It presents the research motivations and the developed framework’s main blocks, which include model-based knowledge management, collaboration service-oriented architectures implemented over a cloud-based solution, and focusing particularly on its negotiation core mechanism to handle inconsistencies and solutions for the detected interoperability problems. It concludes by validating the research and the proposed framework, presenting its application in a real business case of aerospace mission design on the European Space Agency (ESA).FP7 ENSEMBLE, UNITE, MSEE and IMAGINE project

Integrating Peer-to-Peer Networking and Computing in the AgentScape Framework

The combination of peer-to-peer networking and agentbased computing seems to be a perfect match. Agents are cooperative and communication oriented, while peerto -peer networks typically support distributed systems in which all nodes have equal roles and responsibilities. AgentScape is a framework designed to support large-scale multi-agent systems. Pole extends this framework with peerto -peer computing. This combination facilitates the development and deployment of new agent-based peer-to-peer applications and services

Preliminary specification and design documentation for software components to achieve catallaxy in computational systems

This Report is about the preliminary specifications and design documentation for software components to achieve Catallaxy in computational systems. -- Die Arbeit beschreibt die Spezifikation und das Design von Softwarekomponenten, um das Konzept der Katallaxie in Grid Systemen umzusetzen. Eine Einführung ordnet das Konzept der Katallaxie in bestehende Grid Taxonomien ein und stellt grundlegende Komponenten vor. Anschließend werden diese Komponenten auf ihre Anwendbarkeit in bestehenden Application Layer Netzwerken untersucht.Grid Computing

Molecular phylogenetic analysis: design and implementation of scalable and reliable algorithms and verification of phylogenetic properties

El término bioinformática tiene muchas acepciones, una gran parte referentes a la bioinformática molecular: el conjunto de métodos matemáticos, estadísticos y computacionales que tienen como objetivo dar solución a problemas biológicos, haciendo uso exclusivamente de las secuencias de ADN, ARN y proteínas y su información asociada. La filogenética es el área de la bioinformática encargada del estudio de la relación evolutiva entre organismos de la misma o distintas especies. Al igual que sucedía con la definición anterior, los trabajos realizados a lo largo de esta tesis se centran en la filogenética molecular: la rama de la filogenética que analiza las mutaciones hereditarias en secuencias biológicas (principalmente ADN) para establecer dicha relación evolutiva. El resultado de este análisis se plasma en un árbol evolutivo o filogenia. Una filogenia suele representarse como un árbol con raíz, normalmente binario, en el que las hojas simbolizan los organismos existentes actualmente y, la raíz, su ancestro común. Cada nodo interno representa una mutación que ha dado lugar a una división en la clasificación de los descendientes. Las filogenias se construyen mediante procesos de inferencia en base a la información disponible, que pertenece mayoritariamente a organismos existentes hoy en día. La complejidad de este problema se ha visto reflejada en la clasificación de la mayoría de métodos propuestos para su solución como NP-duros [1-3].El caso real de aplicación de esta tesis ha sido el ADN mitocondrial. Este tipo de secuencias biológicas es relevante debido a que tiene un alto índice de mutación, por lo que incluso filogenias de organismos muy cercanos evolutivamente proporcionan datos significativos para la comunidad biológica. Además, varias mutaciones del ADN mitocondrial humano se han relacionado directamente con enfermedad y patogenias, la mayoría mortales en individuos no natos o de corta edad. En la actualidad hay más de 30000 secuencias disponibles de ADN mitocondrial humano, lo que, además de su utilidad científica, ha permitido el análisis de rendimiento de nuestras contribuciones para datos masivos (Big Data). La reciente incorporación de la bioinformática en la categoría Big Data viene respaldada por la mejora de las técnicas de digitalización de secuencias biológicas que sucedió a principios del siglo 21 [4]. Este cambio aumentó drásticamente el número de secuencias disponibles. Por ejemplo, el número de secuencias de ADN mitocondrial humano pasó de duplicarse cada cuatro años, a hacerlo en menos de dos. Por ello, un gran número de métodos y herramientas usados hasta entonces han quedado obsoletos al no ser capaces de procesar eficientemente estos nuevos volúmenes de datos.Este es motivo por el que todas las aportaciones de esta tesis han sido desarrolladas para poder tratar grandes volúmenes de datos. La contribución principal de esta tesis es un framework que permite diseñar y ejecutar automáticamente flujos de trabajo para la inferencia filogenética: PhyloFlow [5-7]. Su creación fue promovida por el hecho de que la mayoría de sistemas de inferencia filogenética existentes tienen un flujo de trabajo fijo y no se pueden modificar ni las herramientas software que los componen ni sus parámetros. Esta decisión puede afectar negativamente a la precisión del resultado si el flujo del sistema o alguno de sus componentes no está adaptado a la información biológica que se va a utilizar como entrada. Por ello, PhyloFlow incorpora un proceso de configuración que permite seleccionar tanto cada uno de los procesos que formarán parte del sistema final, como las herramientas y métodos específicos y sus parámetros. Se han incluido consejos y opciones por defecto durante el proceso de configuración para facilitar su uso, sobre todo a usuarios nóveles. Además, nuestro framework permite la ejecución desatendida de los sistemas filogenéticos generados, tanto en ordenadores de sobremesa como en plataformas hardware (clusters, computación en la nube, etc.). Finalmente, se han evaluado las capacidades de PhyloFlow tanto en la reproducción de sistemas de inferencia filogenética publicados anteriormente como en la creación de sistemas orientados a problemas intensivos como el de inferencia del ADN mitocondrial humano. Los resultados muestran que nuestro framework no solo es capaz de realizar los retos planteados, sino que, en el caso de la replicación de sistemas, la posibilidad de configurar cada elemento que los componen mejora ampliamente su aplicabilidad.Durante la implementación de PhyloFlow descubrimos varias carencias importantes en algunas bibliotecas software actuales que dificultaron la integración y gestión de las herramientas filogenéticas. Por este motivo se decidió crear la primera biblioteca software en Python para estudios de filogenética molecular: MEvoLib [8]. Esta biblioteca ha sido diseñada para proveer una sola interfaz para los conjuntos de herramientas software orientados al mismo proceso, como el multialineamiento o la inferencia de filogenias. MEvoLib incluye además configuraciones por defecto y métodos que hacen uso de conocimiento biológico específico para mejorar su precisión, adaptándose a las necesidades de cada tipo de usuario. Como última característica relevante, se ha incorporado un proceso de conversión de formatos para los ficheros de entrada y salida de cada interfaz, de forma que, si la herramienta seleccionada no soporta dicho formato, este es adaptado automáticamente. Esta propiedad facilita el uso e integración de MEvoLib en scripts y herramientas software.El estudio del caso de aplicación de PhyloFlow al ADN mitocondrial humano ha expuesto los elevados costes tanto computacionales como económicos asociados a la inferencia de grandes filogenias. Por ello, sistemas como PhyloTree [9], que infiere un tipo especial de filogenias de ADN mitocondrial humano, recalculan sus resultados con una frecuencia máxima anual. Sin embargo, como ya hemos comentado anteriormente, las técnicas de secuenciación actuales permiten la incorporación de cientos o incluso miles de secuencias biológicas nuevas cada mes. Este desfase entre productor y consumidor hace que dichas filogenias queden desactualizadas en unos pocos meses. Para solucionar este problema hemos diseñado un nuevo algoritmo que permite la actualización de una filogenia mediante la incorporación iterativa de nuevas secuencias: PHYSER [10]. Además, la propia información evolutiva se utiliza para detectar posibles mutaciones introducidas artificialmente por el proceso de secuenciación, inexistentes en la secuencia original. Las pruebas realizadas con ADN mitocondrial han probado su eficacia y eficiencia, con un coste temporal por secuencia inferior a los 20 segundos.El desarrollo de nuevas herramientas para el análisis de filogenias también ha sido una parte importante de esta tesis. En concreto, se han realizado dos aportaciones principales en este aspecto: PhyloViewer [11] y una herramienta para el análisis de la conservación [12]. PhyloViewer es un visualizador de filogenias extensivas, es decir, filogenias que poseen al menos un millar de hojas. Esta herramienta aporta una novedosa interfaz en la que se muestra el nodo seleccionado y sus nodos hijo, así como toda la información asociada a cada uno de ellos: identificador, secuencia biológica, ... Esta decisión de diseño ha sido orientada a evitar el habitual “borrón” que se produce en la mayoría de herramientas de visualización al mostrar este tipo de filogenias enteras por pantalla. Además, se ha desarrollado en una arquitectura clienteservidor, con lo que el procesamiento de la filogenia se realiza una única vez por parte el servidor. Así, se ha conseguido reducir significativamente los tiempos de carga y acceso por parte del cliente. Por otro lado, la aportación principal de nuestra herramienta para el análisis de la conservación se basa en la paralelización de los métodos clásicos aplicados en este campo, alcanzando speed-ups cercanos al teórico sin pérdida de precisión. Esto ha sido posible gracias a la implementación de dichos métodos desde cero, incorporando la paralelización a nivel de instrucción, en vez de paralelizar implementaciones existentes. Como resultado, nuestra herramienta genera un informe que contiene las conclusiones del análisis de conservación realizado. El usuario puede introducir un umbral de conservación para que el informe destaque solo aquellas posiciones que no lo cumplan. Además, existen dos tipos de informe con distinto nivel de detalle. Ambos se han diseñado para que sean comprensibles y útiles para los usuarios.Finalmente, se ha diseñado e implementado un predictor de mutaciones patógenas en ADN mitocondrial desarollado en máquinas de vectores de soporte (SVM): Mitoclass.1 [13]. Se trata del primer predictor para este tipo de secuencias biológicas. Tanto es así, que ha sido necesario crear el primer repositorio de mutaciones patógenas conocidas, mdmv.1, para poder entrenar y evaluar nuestro predictor. Se ha demostrado que Mitoclass.1 mejora la clasificación de las mutaciones frente a los predictores más conocidos y utilizados, todos ellos orientados al estudio de patogenicidad en ADN nuclear. Este éxito radica en la novedosa combinación de propiedades a evaluar por cada mutación en el proceso de clasificación. Además, otro factor a destacar es el uso de SVM frente a otras alternativas, que han sido probadas y descartadas debido a su menor capacidad de predicción para nuestro caso de aplicación.REFERENCIAS[1] L. Wang and T. Jiang, “On the complexity of multiple sequence alignment,” Journal of computational biology, vol. 1, no. 4, pp. 337–348, 1994.[2] W. H. E. Day, D. S. Johnson, and D. Sankoff, “The Computational Complexity of Inferring Rooted Phylogenies by Parsimony,” Mathematical Biosciences, vol. 81, no. 1, pp. 33–42, 1986.[3] S. Roch, “A short proof that phylogenetic tree reconstruction by maximum likelihood is hard,” IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol. 3, no. 1, p. 92, 2006.[4] E. R. Mardis, “The impact of next-generation sequencing technology on genetics,” Trends in genetics, vol. 24, no. 3, pp. 133–141, 2008.[5] J. Álvarez-Jarreta, G. de Miguel Casado, and E. Mayordomo, “PhyloFlow: A Fully Customizable and Automatic Workflow for Phylogeny Estimation,” in ECCB 2014, 2014.[6] J. Álvarez-Jarreta, G. de Miguel Casado, and E. Mayordomo, “PhyloFlow: A Fully Customizable and Automatic Workflow for Phylogenetic Reconstruction,” in IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 1–7, IEEE, 2014.[7] J. Álvarez, R. Blanco, and E. Mayordomo, “Workflows with Model Selection: A Multilocus Approach to Phylogenetic Analysis,” in 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011), vol. 93 of Advances in Intelligent and Soft Computing, pp. 39–47, Springer Berlin Heidelberg, 2011.[8] J. Álvarez-Jarreta and E. Ruiz-Pesini, “MEvoLib v1.0: the First Molecular Evolution Library for Python,” BMC Bioinformatics, vol. 17, no. 436, pp. 1–8, 2016.[9] M. van Oven and M. Kayser, “Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation,” Human Mutation, vol. 30, no. 2, pp. E386–E394, 2009.[10] J. Álvarez-Jarreta, E. Mayordomo, and E. Ruiz-Pesini, “PHYSER: An Algorithm to Detect Sequencing Errors from Phylogenetic Information,” in 6th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2012), pp. 105–112, 2012.[11] J. Álvarez-Jarreta and G. de Miguel Casado, “PhyloViewer: A Phylogenetic Tree Viewer for Extense Phylogenies,” in ECCB 2014, 2014.[12] F. Merino-Casallo, J. Álvarez-Jarreta, and E. Mayordomo, “Conservation in mitochondrial DNA: Parallelized estimation and alignment influence,” in 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015), pp. 1434–1440, IEEE, 2015.[13] A. Martín-Navarro, A. Gaudioso-Simón, J. Álvarez-Jarreta, J. Montoya, E. Mayordomo, and E. Ruiz-Pesini, “Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides,” BMC Bioinformatics, vol. 18, no. 158, pp. 1–11, 2017.<br /

Situation Management with Complex Event Processing

With the broader dissemination of digital technologies, visionary concepts like the Internet of Things also affect an increasing number of use cases with interfaces to humans, e.g. manufacturing environments with technical operators monitoring the processes. This leads to additional challenges, as besides the technical issues also human aspects have to be considered for a successful implementation of strategic initiatives like Industrie 4.0. From a technical perspective, complex event processing has proven itself in practice to be capable of integrating and analyzing huge amounts of heterogeneous data and establishing a basic level of situation awareness by detecting situations of interests. Whereas this reactive nature of complex event processing systems may be sufficient for machine-to-machine use cases, the new characteristic of application fields with humans remaining in the control loop leads to an increasing action distance and delayed reactions. Taking human aspects into consideration leads to new requirements, with transparency and comprehensibility of the processing of events being the most important ones. Improving the comprehensibility of complex event processing and extending its capabilities towards an effective support of human operators allows tackling technical and non-technical challenges at the same time. The main contribution of this thesis answers the question of how to evolve state-of-the-art complex event processing from its reactive nature towards a transparent and holistic situation management system. The goal is to improve the interaction among systems and humans in use cases with interfaces between both worlds. Realizing a holistic situation management requires three missing capabilities to be introduced by the contributions of this thesis: First, based on the achieved transparency, the retrospective analysis of situations is enabled by collecting information related to a situation\u27s occurrence and development. Therefore, CEP engine-specific situation descriptions are transformed into a common model, allowing the automatic decomposition of the underlying patterns to derive partial patterns describing the intermediate states of processing. Second, by introducing the psychological model of situation awareness into complex event processing, human aspects of information processing are taken into consideration and introduced into the complex event processing paradigm. Based on this model, an extended situation life-cycle and transition method are derived. The introduced concepts and methods allow the implementation of the controlling function of situation management and enable the effective acquisition and maintenance of situation awareness for human operators to purposefully direct their attention towards upcoming situations. Finally, completing the set of capabilities for situation management, an approach is presented to support the generation and integration of prediction models for predictive situation management. Therefore, methods are introduced to automatically label and extract relevant data for the generation of prediction models and to enable the embedding of the resulting models for an automatic evaluation and execution. The contributions are introduced, applied and evaluated along a scenario from the manufacturing domain

Integrated and Decentralized Project Management

Software has become a prominent aspect of the modern world, as it is present and constantly aids people in their daily lives. Consequently, the software development industry has grown in size and competitiveness. Software companies, more than ever, need to keep the best practices for quick and efficient delivery, low maintenance, and overall better profit to succeed in such market. For this very reason, several project management techniques have been developed and put into practice over the years. Nevertheless, its utmost focus has to generate effective arranging of resources and tasks and turn it into the desired end product. Moreover, the selection of an adequate management techniques (taking into account the company and the project’s background) allows the result to better fit into the defined requirements and objectives and improve workflow and productivity along the way. However, the software development field and the project management itself became complex, containing several steps, rules, and involved parties. All this can lead to unorganized data, and an easy disruption of the management workflow. These problems, not only depend on the company’s culture but also on the multiple tools used to ensure proper planning and coordination. Thus, the correct and justified integration to other company’s tools create a synergistic environment from which the firm would benefit. In other words, the integration of specialized systems would enable a better project management - as not only the relevant and necessary information would be up-to-date throughout all systems, but also, workload would be correctly distributed by all employees. This report demonstrates a possible approach to this problem and describes the several phases to achieve the solution - from requirements gathering, analysis and research, and the design and development of a software project management system. Subsequently, the conceptualized solution is based in the current project management application used in Armis. However, it now integrates with the company’s customer relationship management application, as well as the financial software. Moreover, it provides a better, more controlled and organized sequence of actions of the management processes. The developed application comprises of a proof of concept based on the conceptualized solution. It was later evaluated and tested to assess its suitability and conformity with the proposed goals.Produtos de software tornaram-se peças fundamentais do mundo atual, estando presente e auxiliando as pessoas até na mais pequena tarefa. Consequentemente, a indústria de desenvolvimento de software tem crescido consideravelmente, tornando-se assim um ambiente bastante competitivo. De forma a garantir a sua sobrevivência e sucesso no mercado, estas organizações precisam de adotar as melhores práticas para que exista não só uma entrega de produto rápida e eficiente, mas também baixos custos de manutenção do mesmo e maior lucro. Assim, ao longo do tempo foram desenvolvidas e testadas várias técnicas de gestão de projetos. É de extrema importância a adoção de uma boa técnica de gestão, sempre considerando as práticas exercidas e a experiência da empresa, assim como o projeto em questão. Desta forma, o resultado final enquadrar-se-á nos requisitos e objetivos estabelecidos, consequente de um aumento da produtividade e melhor fluxo de trabalho. No entanto, a área de desenvolvimento de software e também da gestão de projetos tem-se tornado mais complexa ao longo dos anos, incluindo cada vez mais passos, regras e pessoas envolvidas no processo. Tudo isso pode levar à desorganização da informação relevante e à fácil interrupção do fluxo de trabalho na gestão de projetos. Esses problemas não dependem apenas da cultura organizacional, mas também das várias ferramentas utilizadas na gestão e coordenação de recursos. Assim, a integração correta e justificada às outras ferramentas da empresa cria um ambiente sinérgico, o qual seria vantajoso para a organização. Por outras palavras, a integração de sistemas especializados permitiria uma melhor gestão dos projetos - sendo que, não só as informações relevantes e necessárias estariam atualizadas em todos os sistemas, mas também a carga de trabalho seria distribuída corretamente por todos os funcionários. Este documento descreve uma solução possível ao problema exposto e descreve as várias fases para alcançar a solução - desde o levantamento de requisitos, análises e pesquisas, e design e desenvolvimento de um sistema de gestão de projetos de software. Posteriormente, a solução preconizada é baseada na ferramenta de gestão de projetos atualmente utilizada na Armis. No entanto, a solução integra agora outras ferramentas utilizadas pela empresa: a aplicação de gestão de clientes, assim como o software financeiro. Além disso, proporciona uma sequência melhor, mais controlada e organizada de ações relativos aos processos de gestão. A aplicação desenvolvida corresponde a uma prova de conceito baseada na solução idealizada, que, posteriormente, foi avaliada e devidamente testada para confirmar a sua adequabilidade e conformidade com os objetivos previamente definidos

3G migration in Pakistan

The telecommunication industry in Pakistan has come a long way since the country\u27s independence in 1947. The initial era could be fairly termed as the PTCL (Pakistan Telecommunication Company Limited) monopoly, for it was the sole provider of all telecommunication services across the country. It was not until four decades later that the region embarked into the new world of wireless communication, hence ending the decades old PTCL monopoly. By the end of the late 1990\u27s, government support and international investment in the region opened new doors to innovation and better quality, low cost, healthy competition. Wireless licenses for the private sector in the telecommunication industry triggered a promising chain of events that resulted in a drastic change in the telecommunication infrastructure and service profile. The newly introduced wireless (GSM) technology received enormous support from all stakeholders (consumers, regulatory body, and market) and caused a vital boost in Pakistan\u27s economy. Numerous tangential elements had triggered this vital move in the history of telecommunications in Pakistan. Entrepreneurs intended to test the idea of global joint ventures in the East and hence the idea of international business became a reality. The technology had proven to be a great success in the West, while Pakistan\u27s telecom consumer had lived under the shadow of PTCL dominance for decades and needed more flexibility. At last the world was moving from wired to wireless! Analysts termed this move as the beginning of a new era. The investors, telecommunication businesses, and Pakistani treasury prospered. It was a win-win situation for all involved. The learning curve was steep for both operators and consumers but certainly improved over time. In essence, the principle of deploying the right technology in the right market at the right time led to this remarkable success. The industry today stands on the brink of a similar crossroads via transition from second generation to something beyond. With the partial success of 3G in Europe and the USA, the government has announced the release of three 3G licenses by mid 2009. This decision is not yet fully supported by all but still initiated parallel efforts by the operators and the vendors to integrate this next move into their existing infrastructure