The swelling behaviour of polyelectrolyte networks

Being basic ingredients of numerous daily-life products with significant industrial importance as well as basic building blocks for biomaterials, charged hydrogels continue to pose a series of unanswered challenges for scientists even after decades of practical applications and intensive research efforts. Despite a rather simple internal structure it is mainly the unique combination of short- and long-range forces which render scientific investigations of their characteristic properties to be quite difficult. Hence early on computer simulations were used to link analytical theory and empirical experiments, bridging the gap between the simplifying assumptions of the models and the complexity of real world measurements. Due to the immense numerical effort, even for high performance supercomputers, system sizes and time scales were rather restricted until recently, whereas it only now has become possible to also simulate a network of charged macromolecules. This is the topic of the presented thesis which investigates one of the fundamental and at the same time highly fascinating phenomenon of polymer research: The swelling behaviour of polyelectrolyte networks. For this an extensible simulation package for the research on soft matter systems, ESPResSo for short, was created which puts a particular emphasis on mesoscopic bead-spring-models of complex systems. Highly efficient algorithms and a consistent parallelization reduced the necessary computation time for solving equations of motion even in case of long-ranged electrostatics and large number of particles, allowing to tackle even expensive calculations and applications. Nevertheless, the program has a modular and simple structure, enabling a continuous process of adding new potentials, interactions, degrees of freedom, ensembles, and integrators, while staying easily accessible for newcomers due to a Tcl-script steering level controlling the C-implemented simulation core. Numerous analysis routines provide means to investigate system properties and observables on-the-fly. Even though analytical theories agreed on the modeling of networks in the past years, our numerical MD-simulations show that even in case of simple model systems fundamental theoretical assumptions no longer apply except for a small parameter regime, prohibiting correct predictions of observables. Applying a "microscopic" analysis of the isolated contributions of individual system components, one of the particular strengths of computer simulations, it was then possible to describe the behaviour of charged polymer networks at swelling equilibrium in good solvent and close to the Theta-point by introducing appropriate model modifications. This became possible by enhancing known simple scaling arguments with components deemed crucial in our detailed study, through which a generalized model could be constructed. Herewith an agreement of the final system volume of swollen polyelectrolyte gels with results of computer simulations could be shown successfully over the entire investigated range of parameters, for different network sizes, charge fractions, and interaction strengths. In addition, the "cell under tension" was presented as a self-regulating approach for predicting the amount of swelling based on the used system parameters only. Without the need for measured observables as input, minimizing the free energy alone already allows to determine the the equilibrium behaviour. In poor solvent the shape of the network chains changes considerably, as now their hydrophobicity counteracts the repulsion of like-wise charged monomers and pursues collapsing the polyelectrolytes. Depending on the chosen parameters a fragile balance emerges, giving rise to fascinating geometrical structures such as the so-called pear-necklaces. This behaviour, known from single chain polyelectrolytes under similar environmental conditions and also theoretically predicted, could be detected for the first time for networks as well. An analysis of the total structure factors confirmed first evidences for the existence of such structures found in experimental results.

Cache-aware development of high integrity real-time systems

Cost, performance and availability considerations are forcing even the most conservative high-integrity embedded real-time systems industry to migrate from simple hardware processors to ones equipped with caches and other acceleration features. This migration disrupts the practices and solutions that industry had developed and consolidated over the years to perform timing analysis. Industry that are confident with the efficiency/effectiveness of their verification and validation processes for old-generation processors, do not have sufficient insight on the effects of the migration to cache-equipped processors. Caches are perceived as an additional source of complexity, which has potential for shattering the guarantees of cost- and schedule-constrained qualification of their systems. The current industrial approach to timing analysis is ill-equipped to cope with the variability incurred by caches. Conversely, the application of advanced WCET analysis techniques on real-world industrial software, developed without analysability in mind, is hardly feasible. We propose a development approach aimed at minimising the cache jitters, as well as at enabling the application of advanced WCET analysis techniques to industrial systems. Our approach builds on:(i) identification of those software constructs that may impede or complicate timing analysis in industrial-scale systems; (ii) elaboration of practical means, under the model-driven engineering (MDE) paradigm, to enforce the automated generation of software that is analyzable by construction; (iii) implementation of a layout optimisation method to remove cache jitters stemming from the software layout in memory, with the intent of facilitating incremental software development, which is of high strategic interest to industry. The integration of those constituents in a structured approach to timing analysis achieves two interesting properties: the resulting software is analysable from the earliest releases onwards - as opposed to becoming so only when the system is final - and more easily amenable to advanced timing analysis by construction, regardless of the system scale and complexity.

Middleware for quality-based context distribution in mobile systems

The continuous advancements and enhancements of wireless systems are enabling new compelling scenarios where mobile services can adapt according to the current execution context, represented by the computational resources available at the local device, current physical location, people in physical proximity, and so forth. Such services called context-aware require the timely delivery of all relevant information describing the current context, and that introduces several unsolved complexities, spanning from low-level context data transmission up to context data storage and replication into the mobile system. In addition, to ensure correct and scalable context provisioning, it is crucial to integrate and interoperate with different wireless technologies (WiFi, Bluetooth, etc.) and modes (infrastructure-based and ad-hoc), and to use decentralized solutions to store and replicate context data on mobile devices. These challenges call for novel middleware solutions, here called Context Data Distribution Infrastructures (CDDIs), capable of delivering relevant context data to mobile devices, while hiding all the issues introduced by data distribution in heterogeneous and large-scale mobile settings. This dissertation thoroughly analyzes CDDIs for mobile systems, with the main goal of achieving a holistic approach to the design of such type of middleware solutions. We discuss the main functions needed by context data distribution in large mobile systems, and we claim the precise definition and clean respect of quality-based contracts between context consumers and CDDI to reconfigure main middleware components at runtime. We present the design and the implementation of our proposals, both in simulation-based and in real-world scenarios, along with an extensive evaluation that confirms the technical soundness of proposed CDDI solutions. Finally, we consider three highly heterogeneous scenarios, namely disaster areas, smart campuses, and smart cities, to better remark the wide technical validity of our analysis and solutions under different network deployments and quality constraints.

Operating System Contribution to Composable Timing Behaviour in High-Integrity Real-Time Systems

The development of High-Integrity Real-Time Systems has a high footprint in terms of human, material and schedule costs. Factoring functional, reusable logic in the application favors incremental development and contains costs. Yet, achieving incrementality in the timing behavior is a much harder problem. Complex features at all levels of the execution stack, aimed to boost average-case performance, exhibit timing behavior highly dependent on execution history, which wrecks time composability and incrementaility with it. Our goal here is to restitute time composability to the execution stack, working bottom up across it. We first characterize time composability without making assumptions on the system architecture or the software deployment to it. Later, we focus on the role played by the real-time operating system in our pursuit. Initially we consider single-core processors and, becoming less permissive on the admissible hardware features, we devise solutions that restore a convincing degree of time composability. To show what can be done for real, we developed TiCOS, an ARINC-compliant kernel, and re-designed ORK+, a kernel for Ada Ravenscar runtimes. In that work, we added support for limited-preemption to ORK+, an absolute premiere in the landscape of real-word kernels. Our implementation allows resource sharing to co-exist with limited-preemptive scheduling, which extends state of the art. We then turn our attention to multicore architectures, first considering partitioned systems, for which we achieve results close to those obtained for single-core processors. Subsequently, we shy away from the over-provision of those systems and consider less restrictive uses of homogeneous multiprocessors, where the scheduling algorithm is key to high schedulable utilization. To that end we single out RUN, a promising baseline, and extend it to SPRINT, which supports sporadic task sets, hence matches real-world industrial needs better. To corroborate our results we present findings from real-world case studies from avionic industry.

Optimized scheduling in real-time environments with column generation

Im Bereich sicherheitsrelevanter eingebetteter Systeme stellt sich der Designprozess von Anwendungen als sehr komplex dar. Entsprechend einer gegebenen Hardwarearchitektur lassen sich Steuergeräte aufrüsten, um alle bestehenden Prozesse und Signale pünktlich auszuführen. Die zeitlichen Anforderungen sind strikt und müssen in jeder periodischen Wiederkehr der Prozesse erfüllt sein, da die Sicherstellung der parallelen Ausführung von größter Bedeutung ist. Existierende Ansätze können schnell Designalternativen berechnen, aber sie gewährleisten nicht, dass die Kosten für die nötigen Hardwareänderungen minimal sind. Wir stellen einen Ansatz vor, der kostenminimale Lösungen für das Problem berechnet, die alle zeitlichen Bedingungen erfüllen. Unser Algorithmus verwendet Lineare Programmierung mit Spaltengenerierung, eingebettet in eine Baumstruktur, um untere und obere Schranken während des Optimierungsprozesses bereitzustellen. Die komplexen Randbedingungen zur Gewährleistung der periodischen Ausführung verlagern sich durch eine Zerlegung des Hauptproblems in unabhängige Unterprobleme, die als ganzzahlige lineare Programme formuliert sind. Sowohl die Analysen zur Prozessausführung als auch die Methoden zur Signalübertragung werden untersucht und linearisierte Darstellungen angegeben. Des Weiteren präsentieren wir eine neue Formulierung für die Ausführung mit fixierten Prioritäten, die zusätzlich Prozessantwortzeiten im schlimmsten anzunehmenden Fall berechnet, welche für Szenarien nötig sind, in denen zeitliche Bedingungen an Teilmengen von Prozessen und Signalen gegeben sind. Wir weisen die Anwendbarkeit unserer Methoden durch die Analyse von Instanzen nach, welche Prozessstrukturen aus realen Anwendungen enthalten. Unsere Ergebnisse zeigen, dass untere Schranken schnell berechnet werden können, um die Optimalität von heuristischen Lösungen zu beweisen. Wenn wir optimale Lösungen mit Antwortzeiten liefern, stellt sich unsere neue Formulierung in der Laufzeitanalyse vorteilhaft gegenüber anderen Ansätzen dar. Die besten Resultate werden mit einem hybriden Ansatz erzielt, der heuristische Startlösungen, eine Vorverarbeitung und eine heuristische mit einer kurzen nachfolgenden exakten Berechnungsphase verbindet.

USING PROBABILISTIC GRAPHICAL MODELS TO DRAW INFERENCES IN SENSOR NETWORKS WITH TRACKING APPLICATIONS

Sensor networks have been an active research area in the past decade due to the variety of their applications. Many research studies have been conducted to solve the problems underlying the middleware services of sensor networks, such as self-deployment, self-localization, and synchronization. With the provided middleware services, sensor networks have grown into a mature technology to be used as a detection and surveillance paradigm for many real-world applications. The individual sensors are small in size. Thus, they can be deployed in areas with limited space to make unobstructed measurements in locations where the traditional centralized systems would have trouble to reach. However, there are a few physical limitations to sensor networks, which can prevent sensors from performing at their maximum potential. Individual sensors have limited power supply, the wireless band can get very cluttered when multiple sensors try to transmit at the same time. Furthermore, the individual sensors have limited communication range, so the network may not have a 1-hop communication topology and routing can be a problem in many cases. Carefully designed algorithms can alleviate the physical limitations of sensor networks, and allow them to be utilized to their full potential. Graphical models are an intuitive choice for designing sensor network algorithms. This thesis focuses on a classic application in sensor networks, detecting and tracking of targets. It develops feasible inference techniques for sensor networks using statistical graphical model inference, binary sensor detection, events isolation and dynamic clustering. The main strategy is to use only binary data for rough global inferences, and then dynamically form small scale clusters around the target for detailed computations. This framework is then extended to network topology manipulation, so that the framework developed can be applied to tracking in different network topology settings. Finally the system was tested in both simulation and real-world environments. The simulations were performed on various network topologies, from regularly distributed networks to randomly distributed networks. The results show that the algorithm performs well in randomly distributed networks, and hence requires minimum deployment effort. The experiments were carried out in both corridor and open space settings. A in-home falling detection system was simulated with real-world settings, it was setup with 30 bumblebee radars and 30 ultrasonic sensors driven by TI EZ430-RF2500 boards scanning a typical 800 sqft apartment. Bumblebee radars are calibrated to detect the falling of human body, and the two-tier tracking algorithm is used on the ultrasonic sensors to track the location of the elderly people.

Real Walking through Virtual Environments by Redirection Techniques

We present redirection techniques that support exploration of large-scale virtual environments (VEs) by means of real walking. We quantify to what degree users can unknowingly be redirected in order to guide them through VEs in which virtual paths differ from the physical paths. We further introduce the concept of dynamic passive haptics by which any number of virtual objects can be mapped to real physical proxy props having similar haptic properties (i. e., size, shape, and surface structure), such that the user can sense these virtual objects by touching their real world counterparts. Dynamic passive haptics provides the user with the illusion of interacting with a desired virtual object by redirecting her to the corresponding proxy prop. We describe the concepts of generic redirected walking and dynamic passive haptics and present experiments in which we have evaluated these concepts. Furthermore, we discuss implications that have been derived from a user study, and we present approaches that derive physical paths which may vary from the virtual counterparts.

Energy-Efficient Management Of Heterogeneous Wireless Sensor Networks

Various applications for the purposes of event detection, localization, and monitoring can benefit from the use of wireless sensor networks (WSNs). Wireless sensor networks are generally easy to deploy, with flexible topology and can support diversity of tasks thanks to the large variety of sensors that can be attached to the wireless sensor nodes. To guarantee the efficient operation of such a heterogeneous wireless sensor networks during its lifetime an appropriate management is necessary. Typically, there are three management tasks, namely monitoring, (re) configuration, and code updating. On the one hand, status information, such as battery state and node connectivity, of both the wireless sensor network and the sensor nodes has to be monitored. And on the other hand, sensor nodes have to be (re)configured, e.g., setting the sensing interval. Most importantly, new applications have to be deployed as well as bug fixes have to be applied during the network lifetime. All management tasks have to be performed in a reliable, time- and energy-efficient manner. The ability to disseminate data from one sender to multiple receivers in a reliable, time- and energy-efficient manner is critical for the execution of the management tasks, especially for code updating. Using multicast communication in wireless sensor networks is an efficient way to handle such traffic pattern. Due to the nature of code updates a multicast protocol has to support bulky traffic and endto-end reliability. Further, the limited resources of wireless sensor nodes demand an energy-efficient operation of the multicast protocol. Current data dissemination schemes do not fulfil all of the above requirements. In order to close the gap, we designed the Sensor Node Overlay Multicast (SNOMC) protocol such that to support a reliable, time-efficient and energy-efficient dissemination of data from one sender node to multiple receivers. In contrast to other multicast transport protocols, which do not support reliability mechanisms, SNOMC supports end-to-end reliability using a NACK-based reliability mechanism. The mechanism is simple and easy to implement and can significantly reduce the number of transmissions. It is complemented by a data acknowledgement after successful reception of all data fragments by the receiver nodes. In SNOMC three different caching strategies are integrated for an efficient handling of necessary retransmissions, namely, caching on each intermediate node, caching on branching nodes, or caching only on the sender node. Moreover, an option was included to pro-actively request missing fragments. SNOMC was evaluated both in the OMNeT++ simulator and in our in-house real-world testbed and compared to a number of common data dissemination protocols, such as Flooding, MPR, TinyCubus, PSFQ, and both UDP and TCP. The results showed that SNOMC outperforms the selected protocols in terms of transmission time, number of transmitted packets, and energy-consumption. Moreover, we showed that SNOMC performs well with different underlying MAC protocols, which support different levels of reliability and energy-efficiency. Thus, SNOMC can offer a robust, high-performing solution for the efficient distribution of code updates and management information in a wireless sensor network. To address the three management tasks, in this thesis we developed the Management Architecture for Wireless Sensor Networks (MARWIS). MARWIS is specifically designed for the management of heterogeneous wireless sensor networks. A distinguished feature of its design is the use of wireless mesh nodes as backbone, which enables diverse communication platforms and offloading functionality from the sensor nodes to the mesh nodes. This hierarchical architecture allows for efficient operation of the management tasks, due to the organisation of the sensor nodes into small sub-networks each managed by a mesh node. Furthermore, we developed a intuitive -based graphical user interface, which allows non-expert users to easily perform management tasks in the network. In contrast to other management frameworks, such as Mate, MANNA, TinyCubus, or code dissemination protocols, such as Impala, Trickle, and Deluge, MARWIS offers an integrated solution monitoring, configuration and code updating of sensor nodes. Integration of SNOMC into MARWIS further increases performance efficiency of the management tasks. To our knowledge, our approach is the first one, which offers a combination of a management architecture with an efficient overlay multicast transport protocol. This combination of SNOMC and MARWIS supports reliably, time- and energy-efficient operation of a heterogeneous wireless sensor network.

A Research Roadmap for Complementary and Alternative Medicine – What We Need to Know by 2020

Background: The CAMbrella coordination action was funded within the Framework Programme 7. Its aim is to provide a research roadmap for clinical and epidemiological research for complementary and alternative medicine (CAM) that is appropriate for the health needs of European citizens and acceptable to their national research institutes and healthcare providers in both public and private sectors. One major issue in the European research agenda is the demographic change and its impact on health care. Our vision for 2020 is that there is an evidence base that enables European citizens to make informed decisions about CAM, both positive and negative. This roadmap proposes a strategic research agenda for the field of CAM designed to address future European health care challenges. This roadmap is based on the results of CAMbrella’s several work packages, literature reviews and expert discussions including a consensus meeting. Methods: We first conducted a systematic literature review on key issues in clinical and epidemiological research in CAM to identify the general concepts, methods and the strengths and weaknesses of current CAM research. These findings were discussed in a workshop (Castellaro, Italy, September 7–9th 2011) with international CAM experts and strategic and methodological recommendations were defined in order to improve the rigor and relevance of CAM research. These recommendations provide the basis for the research roadmap, which was subsequently discussed in a consensus conference (Järna, Sweden, May 9–11th 2012) with all CAMbrella members and the CAMbrella advisory board. The roadmap was revised after this discussion in CAMbrella Work Package (WP) 7 and finally approved by CAMbrella’s scientific steering committee on September 26th 2012. Results: Our main findings show that CAM is very heterogenous in terms of definitions and legal regulations between the European countries. In addition, citizens’ needs and attitudes towards CAM as well as the use and provision of CAM differ significantly between countries. In terms of research methodology, there was consensus that CAM researchers should make use of all the commonly accepted scientific research methods and employ those with utmost diligence combined in a mixed methods framework. Conclusions: We propose 6 core areas of research that should be investigated to achieve a robust knowledge base and to allow stakeholders to make informed decisions. These are: Research into the prevalence of CAM in Europe: Reviews show that we do not know enough about the circumstances in which CAM is used by Europeans. To enable a common European strategic approach, a clear picture of current use is of the utmost importance. Research into differences regarding citizens’ attitudes and needs towards CAM: Citizens are the driver for CAM utilization. Their needs and views on CAM are a key priority, and their interests must be investigated and addressed in future CAM research. Research into safety of CAM: Safety is a key issue for European citizens. CAM is considered safe, but reliable data is scarce although urgently needed in order to assess the risk and cost-benefit ratio of CAM. Research into the comparative effectiveness of CAM: Everybody needs to know in what situation CAM is a reasonable choice. Therefore, we recommend a clear emphasis on concurrent evaluation of the overall effectiveness of CAM as an additional or alternative treatment strategy in real-world settings. Research into effects of context and meaning: The impact of effects of context and meaning on the outcome of CAM treatments must be investigated; it is likely that they are significant. Research into different models of CAM health care integration: There are different models of CAM being integrated into conventional medicine throughout Europe, each with their respective strengths and limitations. These models should be described and concurrently evaluated; innovative models of CAM provision in health care systems should be one focus for CAM research. We also propose a methodological framework for CAM research. We consider that a framework of mixed methodological approaches is likely to yield the most useful information. In this model, all available research strategies including comparative effectiveness research utilising quantitative and qualitative methods should be considered to enable us to secure the greatest density of knowledge possible. Stakeholders, such as citizens, patients and providers, should be involved in every stage of developing the specific and relevant research questions, study design and the assurance of real-world relevance for the research. Furthermore, structural and sufficient financial support for research into CAM is needed to strengthen CAM research capacity if we wish to understand why it remains so popular within the EU. In order to consider employing CAM as part of the solution to the health care, health creation and self-care challenges we face by 2020, it is vital to obtain a robust picture of CAM use and reliable information about its cost, safety and effectiveness in real-world settings. We need to consider the availability, accessibility and affordability of CAM. We need to engage in research excellence and utilise comparative effectiveness approaches and mixed methods to obtain this data. Our recommendations are both strategic and methodological. They are presented for the consideration of researchers and funders while being designed to answer the important and implicit questions posed by EU citizens currently using CAM in apparently increasing numbers. We propose that the EU actively supports an EUwide strategic approach that facilitates the development of CAM research. This could be achieved in the first instance through funding a European CAM coordinating research office dedicated to foster systematic communication between EU governments, public, charitable and industry funders as well as researchers, citizens and other stakeholders. The aim of this office would be to coordinate research strategy developments and research funding opportunities, as well as to document and disseminate international research activities in this field. With the aim to develop sustainability as second step, a European Centre for CAM should be established that takes over the monitoring and further development of a coordinated research strategy for CAM, as well as it should have funds that can be awarded to foster high quality and robust independent research with a focus on citizens health needs and pan-European collaboration. We wish to establish a solid funding for CAM research to adequately inform health care and health creation decision-making throughout the EU. This centre would ensure that our vision of a common, strategic and scientifically rigorous approach to CAM research becomes our legacy and Europe’s reality. We are confident that our recommendations will serve these essential goals for EU citizens.

The distinction between real and fictional worlds: Investigating individual differences in fantasy understanding

In this paper, two studies are reported in which children’s ability to distinguish reality from fantasy was investigated. In Experiment 1, children of different ages made pairwise comparisons of 12 pictures of fictional figures and 3 photographs of real people by evaluating on a 6-point scale how easily these figures could meet each other. The results revealed that fantasy/reality distinction develops with age: 7–8-year-old showed a fundamental categorical distinction (comparable to that of adults) whereas 3–4-year-old treated the real world like one of many worlds. In Experiment 2, we took an individual differences approach and tested 116 4–5-year-old who performed the same fantasy task. In addition, they were presented with theory-of-mind tasks and tests measuring non-verbal intelligence and language skills. The results showed that, after statistically controlling for age, non-verbal intelligence, and language skills, theory-of-mind abilities still significantly contributed to the prediction of fantasy understanding.

A multimodal tablet-based interface for designing and reviewing 3D engineering models

The ability to view and interact with 3D models has been happening for a long time. However, vision-based 3D modeling has only seen limited success in applications, as it faces many technical challenges. Hand-held mobile devices have changed the way we interact with virtual reality environments. Their high mobility and technical features, such as inertial sensors, cameras and fast processors, are especially attractive for advancing the state of the art in virtual reality systems. Also, their ubiquity and fast Internet connection open a path to distributed and collaborative development. However, such path has not been fully explored in many domains. VR systems for real world engineering contexts are still difficult to use, especially when geographically dispersed engineering teams need to collaboratively visualize and review 3D CAD models. Another challenge is the ability to rendering these environments at the required interactive rates and with high fidelity. In this document it is presented a virtual reality system mobile for visualization, navigation and reviewing large scale 3D CAD models, held under the CEDAR (Collaborative Engineering Design and Review) project. It’s focused on interaction using different navigation modes. The system uses the mobile device's inertial sensors and camera to allow users to navigate through large scale models. IT professionals, architects, civil engineers and oil industry experts were involved in a qualitative assessment of the CEDAR system, in the form of direct user interaction with the prototypes and audio-recorded interviews about the prototypes. The lessons learned are valuable and are presented on this document. Subsequently it was prepared a quantitative study on the different navigation modes to analyze the best mode to use it in a given situation.

Chapter 5 Product Differentiation versus Geographical Differentiation: Evidence from the Pork Processing Industry in China

This chapter attempts to identify whether product differentiation or geographical differentiation is the main source of profit for firms in developing economies by employing a simple idea from the recently developed method of empirical industrial organization. Theoretically, location choice and product choice have been considered as analogues in differentiation, but in the real world, which of these strategies is chosen will result in an immense difference in firm behavior and in the development process of the industry. Development of the technique of empirical industrial organization enabled us to identify market outcomes with endogeneity. A typical case is the market outcome with differentiation, where price or product choice is endogenously determined. Our original survey contains data on market location, differences in product types, and price. The results show that product differentiation rather than geographical differentiation mitigates pressure on price competition, but 70 per cent secures geographical monopoly.

ACGT: advancing clinico-genomic trials on cancer - four years of experience.

The challenges regarding seamless integration of distributed, heterogeneous and multilevel data arising in the context of contemporary, post-genomic clinical trials cannot be effectively addressed with current methodologies. An urgent need exists to access data in a uniform manner, to share information among different clinical and research centers, and to store data in secure repositories assuring the privacy of patients. Advancing Clinico-Genomic Trials (ACGT) was a European Commission funded Integrated Project that aimed at providing tools and methods to enhance the efficiency of clinical trials in the -omics era. The project, now completed after four years of work, involved the development of both a set of methodological approaches as well as tools and services and its testing in the context of real-world clinico-genomic scenarios. This paper describes the main experiences using the ACGT platform and its tools within one such scenario and highlights the very promising results obtained.

Semantic middleware development for the Internet of Things

After the extraordinary spread of the World Wide Web during the last fifteen years, engineers and developers are pushing now the Internet to its next border. A new conception in computer science and networks communication has been burgeoning during roughly the last decade: a world where most of the computers of the future will be extremely downsized, to the point that they will look like dust at its most advanced prototypes. In this vision, every single element of our “real” world has an intelligent tag that carries all their relevant data, effectively mapping the “real” world into a “virtual” one, where all the electronically augmented objects are present, can interact among them and influence with their behaviour that of the other objects, or even the behaviour of a final human user. This is the vision of the Internet of the Future, which also draws ideas of several novel tendencies in computer science and networking, as pervasive computing and the Internet of Things. As it has happened before, materializing a new paradigm that changes the way entities interrelate in this new environment has proved to be a goal full of challenges in the way. Right now the situation is exciting, with a plethora of new developments, proposals and models sprouting every time, often in an uncoordinated, decentralised manner away from any standardization, resembling somehow the status quo of the first developments of advanced computer networking, back in the 60s and the 70s. Usually, a system designed after the Internet of the Future will consist of one or several final user devices attached to these final users, a network –often a Wireless Sensor Network- charged with the task of collecting data for the final user devices, and sometimes a base station sending the data for its further processing to less hardware-constrained computers. When implementing a system designed with the Internet of the Future as a pattern, issues, and more specifically, limitations, that must be faced are numerous: lack of standards for platforms and protocols, processing bottlenecks, low battery lifetime, etc. One of the main objectives of this project is presenting a functional model of how a system based on the paradigms linked to the Internet of the Future works, overcoming some of the difficulties that can be expected and showing a model for a middleware architecture specifically designed for a pervasive, ubiquitous system. This Final Degree Dissertation is divided into several parts. Beginning with an Introduction to the main topics and concepts of this new model, a State of the Art is offered so as to provide a technological background. After that, an example of a semantic and service-oriented middleware is shown; later, a system built by means of this semantic and service-oriented middleware, and other components, is developed, justifying its placement in a particular scenario, describing it and analysing the data obtained from it. Finally, the conclusions inferred from this system and future works that would be good to be tackled are mentioned as well. RESUMEN Tras el extraordinario desarrollo de la Web durante los últimos quince años, ingenieros y desarrolladores empujan Internet hacia su siguiente frontera. Una nueva concepción en la computación y la comunicación a través de las redes ha estado floreciendo durante la última década; un mundo donde la mayoría de los ordenadores del futuro serán extremadamente reducidas de tamaño, hasta el punto que parecerán polvo en sus más avanzado prototipos. En esta visión, cada uno de los elementos de nuestro mundo “real” tiene una etiqueta inteligente que porta sus datos relevantes, mapeando de manera efectiva el mundo “real” en uno “virtual”, donde todos los objetos electrónicamente aumentados están presentes, pueden interactuar entre ellos e influenciar con su comportamiento el de los otros, o incluso el comportamiento del usuario final humano. Ésta es la visión del Internet del Futuro, que también toma ideas de varias tendencias nuevas en las ciencias de la computación y las redes de ordenadores, como la computación omnipresente y el Internet de las Cosas. Como ha sucedido antes, materializar un nuevo paradigma que cambia la manera en que las entidades se interrelacionan en este nuevo entorno ha demostrado ser una meta llena de retos en el camino. Ahora mismo la situación es emocionante, con una plétora de nuevos desarrollos, propuestas y modelos brotando todo el rato, a menudo de una manera descoordinada y descentralizada lejos de cualquier estandarización, recordando de alguna manera el estado de cosas de los primeros desarrollos de redes de ordenadores avanzadas, allá por los años 60 y 70. Normalmente, un sistema diseñado con el Internet del futuro como modelo consistirá en uno o varios dispositivos para usuario final sujetos a estos usuarios finales, una red –a menudo, una red de sensores inalámbricos- encargada de recolectar datos para los dispositivos de usuario final, y a veces una estación base enviando los datos para su consiguiente procesado en ordenadores menos limitados en hardware. Al implementar un sistema diseñado con el Internet del futuro como patrón, los problemas, y más específicamente, las limitaciones que deben enfrentarse son numerosas: falta de estándares para plataformas y protocolos, cuellos de botella en el procesado, bajo tiempo de vida de las baterías, etc. Uno de los principales objetivos de este Proyecto Fin de Carrera es presentar un modelo funcional de cómo trabaja un sistema basado en los paradigmas relacionados al Internet del futuro, superando algunas de las dificultades que pueden esperarse y mostrando un modelo de una arquitectura middleware específicamente diseñado para un sistema omnipresente y ubicuo. Este Proyecto Fin de Carrera está dividido en varias partes. Empezando por una introducción a los principales temas y conceptos de este modelo, un estado del arte es ofrecido para proveer un trasfondo tecnológico. Después de eso, se muestra un ejemplo de middleware semántico orientado a servicios; después, se desarrolla un sistema construido por medio de este middleware semántico orientado a servicios, justificando su localización en un escenario particular, describiéndolo y analizando los datos obtenidos de él. Finalmente, las conclusiones extraídas de este sistema y las futuras tareas que sería bueno tratar también son mencionadas.