Enabling a direct path from end-user specifications to executable protocols in a biology laboratory environment

Biomedical analyses are becoming increasingly complex, with respect to both the type of the data to be produced and the procedures to be executed. This trend is expected to continue in the future. The development of information and protocol management systems that can sustain this challenge is therefore becoming an essential enabling factor for all actors in the field. The use of custom-built solutions that require the biology domain expert to acquire or procure software engineering expertise in the development of the laboratory infrastructure is not fully satisfactory because it incurs undesirable mutual knowledge dependencies between the two camps. We propose instead an infrastructure concept that enables the domain experts to express laboratory protocols using proper domain knowledge, free from the incidence and mediation of the software implementation artefacts. In the system that we propose this is made possible by basing the modelling language on an authoritative domain specific ontology and then using modern model-driven architecture technology to transform the user models in software artefacts ready for execution in a multi-agent based execution platform specialized for biomedical laboratories.

Memory hierarchy and data communication in heterogeneous reconfigurable SoCs

The miniaturization race in the hardware industry aiming at continuous increasing of transistor density on a die does not bring respective application performance improvements any more. One of the most promising alternatives is to exploit a heterogeneous nature of common applications in hardware. Supported by reconfigurable computation, which has already proved its efficiency in accelerating data intensive applications, this concept promises a breakthrough in contemporary technology development. Memory organization in such heterogeneous reconfigurable architectures becomes very critical. Two primary aspects introduce a sophisticated trade-off. On the one hand, a memory subsystem should provide well organized distributed data structure and guarantee the required data bandwidth. On the other hand, it should hide the heterogeneous hardware structure from the end-user, in order to support feasible high-level programmability of the system. This thesis work explores the heterogeneous reconfigurable hardware architectures and presents possible solutions to cope the problem of memory organization and data structure. By the example of the MORPHEUS heterogeneous platform, the discussion follows the complete design cycle, starting from decision making and justification, until hardware realization. Particular emphasis is made on the methods to support high system performance, meet application requirements, and provide a user-friendly programmer interface. As a result, the research introduces a complete heterogeneous platform enhanced with a hierarchical memory organization, which copes with its task by means of separating computation from communication, providing reconfigurable engines with computation and configuration data, and unification of heterogeneous computational devices using local storage buffers. It is distinguished from the related solutions by distributed data-flow organization, specifically engineered mechanisms to operate with data on local domains, particular communication infrastructure based on Network-on-Chip, and thorough methods to prevent computation and communication stalls. In addition, a novel advanced technique to accelerate memory access was developed and implemented.

Adaptive wireless multimedia communication systems

In recent years, due to the rapid convergence of multimedia services, Internet and wireless communications, there has been a growing trend of heterogeneity (in terms of channel bandwidths, mobility levels of terminals, end-user quality-of-service (QoS) requirements) for emerging integrated wired/wireless networks. Moreover, in nowadays systems, a multitude of users coexists within the same network, each of them with his own QoS requirement and bandwidth availability. In this framework, embedded source coding allowing partial decoding at various resolution is an appealing technique for multimedia transmissions. This dissertation includes my PhD research, mainly devoted to the study of embedded multimedia bitstreams in heterogenous networks, developed at the University of Bologna, advised by Prof. O. Andrisano and Prof. A. Conti, and at the University of California, San Diego (UCSD), where I spent eighteen months as a visiting scholar, advised by Prof. L. B. Milstein and Prof. P. C. Cosman. In order to improve the multimedia transmission quality over wireless channels, joint source and channel coding optimization is investigated in a 2D time-frequency resource block for an OFDM system. We show that knowing the order of diversity in time and/or frequency domain can assist image (video) coding in selecting optimal channel code rates (source and channel code rates). Then, adaptive modulation techniques, aimed at maximizing the spectral efficiency, are investigated as another possible solution for improving multimedia transmissions. For both slow and fast adaptive modulations, the effects of imperfect channel estimation errors are evaluated, showing that the fast technique, optimal in ideal systems, might be outperformed by the slow adaptive modulation, when a real test case is considered. Finally, the effects of co-channel interference and approximated bit error probability (BEP) are evaluated in adaptive modulation techniques, providing new decision regions concepts, and showing how the widely used BEP approximations lead to a substantial loss in the overall performance.

Architectures for Context Aware Services in Smart Environments

This thesis deals with Context Aware Services, Smart Environments, Context Management and solutions for Devices and Service Interoperability. Multi-vendor devices offer an increasing number of services and end-user applications that base their value on the ability to exploit the information originating from the surrounding environment by means of an increasing number of embedded sensors, e.g. GPS, compass, RFID readers, cameras and so on. However, usually such devices are not able to exchange information because of the lack of a shared data storage and common information exchange methods. A large number of standards and domain specific building blocks are available and are heavily used in today's products. However, the use of these solutions based on ready-to-use modules is not without problems. The integration and cooperation of different kinds of modules can be daunting because of growing complexity and dependency. In this scenarios it might be interesting to have an infrastructure that makes the coexistence of multi-vendor devices easy, while enabling low cost development and smooth access to services. This sort of technologies glue should reduce both software and hardware integration costs by removing the trouble of interoperability. The result should also lead to faster and simplified design, development and, deployment of cross-domain applications. This thesis is mainly focused on SW architectures supporting context aware service providers especially on the following subjects: - user preferences service adaptation - context management - content management - information interoperability - multivendor device interoperability - communication and connectivity interoperability Experimental activities were carried out in several domains including Cultural Heritage, indoor and personal smart spaces – all of which are considered significant test-beds in Context Aware Computing. The work evolved within european and national projects: on the europen side, I carried out my research activity within EPOCH, the FP6 Network of Excellence on “Processing Open Cultural Heritage” and within SOFIA, a project of the ARTEMIS JU on embedded systems. I worked in cooperation with several international establishments, including the University of Kent, VTT (the Technical Reserarch Center of Finland) and Eurotech. On the national side I contributed to a one-to-one research contract between ARCES and Telecom Italia. The first part of the thesis is focused on problem statement and related work and addresses interoperability issues and related architecture components. The second part is focused on specific architectures and frameworks: - MobiComp: a context management framework that I used in cultural heritage applications - CAB: a context, preference and profile based application broker which I designed within EPOCH Network of Excellence - M3: "Semantic Web based" information sharing infrastructure for smart spaces designed by Nokia within the European project SOFIA - NoTa: a service and transport independent connectivity framework - OSGi: the well known Java based service support framework The final section is dedicated to the middleware, the tools and, the SW agents developed during my Doctorate time to support context-aware services in smart environments.

Technology Development and Consumer Acceptance of Innovation in Fruit Production

Precision Agriculture (PA) and the more specific branch of Precision Horticulture are two very promising sectors. They focus on the use of technologies in agriculture to optimize the use of inputs, so to reach a better efficiency, and minimize waste of resources. This important objective motivated many researchers and companies to search new technology solutions. Sometimes the effort proved to be a good seed, but sometimes an unfeasible idea. So that PA, from its birth more or less 25 years ago, is still a “new” management, interesting for the future, but an actual low adoption rate is still reported by experts and researchers. This work aims to give a contribution in finding the causes of this low adoption rate and proposing a methodological solution to this problem. The first step was to examine prior research about Precision Agriculture adoption, by ex ante and ex post approach. It was supposed as important to find connections between these two phases of a purchase experience. In fact, the ex ante studies dealt with potential consumer’s perceptions before a usage experience occurred, therefore before purchasing a technology, while the ex post studies described the drivers which made a farmer become an end-user of PA technology. Then, an example of consumer research is presented. This was an ex ante research focused on pre-prototype technology for fruit production. This kind of research could give precious information about consumer acceptance before reaching an advanced development phase of the technology, and so to have the possibility to change something with the least financial impact. The final step was to develop the pre-prototype technology that was the subject of the consumer acceptance research and test its technical characteristics.

Engineering Complex Computational Ecosystems

Self-organising pervasive ecosystems of devices are set to become a major vehicle for delivering infrastructure and end-user services. The inherent complexity of such systems poses new challenges to those who want to dominate it by applying the principles of engineering. The recent growth in number and distribution of devices with decent computational and communicational abilities, that suddenly accelerated with the massive diffusion of smartphones and tablets, is delivering a world with a much higher density of devices in space. Also, communication technologies seem to be focussing on short-range device-to-device (P2P) interactions, with technologies such as Bluetooth and Near-Field Communication gaining greater adoption. Locality and situatedness become key to providing the best possible experience to users, and the classic model of a centralised, enormously powerful server gathering and processing data becomes less and less efficient with device density. Accomplishing complex global tasks without a centralised controller responsible of aggregating data, however, is a challenging task. In particular, there is a local-to-global issue that makes the application of engineering principles challenging at least: designing device-local programs that, through interaction, guarantee a certain global service level. In this thesis, we first analyse the state of the art in coordination systems, then motivate the work by describing the main issues of pre-existing tools and practices and identifying the improvements that would benefit the design of such complex software ecosystems. The contribution can be divided in three main branches. First, we introduce a novel simulation toolchain for pervasive ecosystems, designed for allowing good expressiveness still retaining high performance. Second, we leverage existing coordination models and patterns in order to create new spatial structures. Third, we introduce a novel language, based on the existing ``Field Calculus'' and integrated with the aforementioned toolchain, designed to be usable for practical aggregate programming.

Design, development and first evaluation of a client/server system for managing and querying linguistic corpora

This thesis is concerned with the role played by software tools in the analysis and dissemination of linguistic corpora and their contribution to a more widespread adoption of corpora in different fields. Chapter 1 contains an overview of some of the most relevant corpus analysis tools available today, presenting their most interesting features and some of their drawbacks. Chapter 2 begins with an explanation of the reasons why none of the available tools appear to satisfy the requirements of the user community and then continues with technical overview of the current status of the new system developed as part of this work. This presentation is followed by highlights of features that make the system appealing to users and corpus builders (i.e. scholars willing to make their corpora available to the public). The chapter concludes with an indication of future directions for the projects and information on the current availability of the software. Chapter 3 describes the design of an experiment devised to evaluate the usability of the new system in comparison to another corpus tool. Usage of the tool was tested in the context of a documentation task performed on a real assignment during a translation class in a master's degree course. In chapter 4 the findings of the experiment are presented on two levels of analysis: firstly a discussion on how participants interacted with and evaluated the two corpus tools in terms of interface and interaction design, usability and perceived ease of use. Then an analysis follows of how users interacted with corpora to complete the task and what kind of queries they submitted. Finally, some general conclusions are drawn and areas for future work are outlined.

Brain-Computer Interfaces for augmented communication: Asynchronous and adaptive algorithms and evaluation with end users

This thesis aimed at addressing some of the issues that, at the state of the art, avoid the P300-based brain computer interface (BCI) systems to move from research laboratories to end users’ home. An innovative asynchronous classifier has been defined and validated. It relies on the introduction of a set of thresholds in the classifier, and such thresholds have been assessed considering the distributions of score values relating to target, non-target stimuli and epochs of voluntary no-control. With the asynchronous classifier, a P300-based BCI system can adapt its speed to the current state of the user and can automatically suspend the control when the user diverts his attention from the stimulation interface. Since EEG signals are non-stationary and show inherent variability, in order to make long-term use of BCI possible, it is important to track changes in ongoing EEG activity and to adapt BCI model parameters accordingly. To this aim, the asynchronous classifier has been subsequently improved by introducing a self-calibration algorithm for the continuous and unsupervised recalibration of the subjective control parameters. Finally an index for the online monitoring of the EEG quality has been defined and validated in order to detect potential problems and system failures. This thesis ends with the description of a translational work involving end users (people with amyotrophic lateral sclerosis-ALS). Focusing on the concepts of the user centered design approach, the phases relating to the design, the development and the validation of an innovative assistive device have been described. The proposed assistive technology (AT) has been specifically designed to meet the needs of people with ALS during the different phases of the disease (i.e. the degree of motor abilities impairment). Indeed, the AT can be accessed with several input devices either conventional (mouse, touchscreen) or alterative (switches, headtracker) up to a P300-based BCI.