Semantic integration of gene expression analysis tools and data sources using software connectors

Abstract Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data.

Prediction of clinical toxicity in locally advanced head and neck cancer patients by radio-induced apoptosis in peripheral blood lymphocytes (PBLs)

[EN] Head and neck cancer is treated mainly by surgery and radiotherapy. Normal tissue toxicity due to x-ray exposure is a limiting factor for treatment success. Many efforts have been employed to develop predictive tests applied to clinical practice. Determination of lymphocyte radio-sensitivity by radio-induced apoptosis arises as a possible method to predict tissue toxicity due to radiotherapy. The aim of the present study was to analyze radio-induced apoptosis of peripheral blood lymphocytes in head and neck cancer patients and to explore their role in predicting radiation induced toxicity. Seventy nine consecutive patients suffering from head and neck cancer, diagnosed and treated in our institution, were included in the study. Toxicity was evaluated using the Radiation Therapy Oncology Group scale. Peripheral blood lymphocytes were isolated and irradiated at 0, 1, 2 and 8 Gy during 24 hours. Apoptosis was measured by flow cytometry using annexin V/propidium iodide. Lymphocytes were marked with CD45 APC-conjugated monoclonal antibody. Radiation-induced apoptosis increased in order to radiation dose and fitted to a semi logarithmic model defined by two constants: α and β. α, as the origin of the curve in the Y axis determining the percentage of spontaneous cell death, and β, as the slope of the curve determining the percentage of cell death induced at a determined radiation dose, were obtained. β value was statistically associated to normal tissue toxicity in terms of severe xerostomia, as higher levels of apoptosis were observed in patients with low toxicity (p = 0.035; Exp(B) 0.224, I.C.95% (0.060-0.904)). These data agree with our previous results and suggest that it is possible to estimate the radiosensitivity of peripheral blood lymphocytes from patients determining the radiation induced apoptosis with annexin V/propidium iodide staining. β values observed define an individual radiosensitivity profile that could predict late toxicity due to radiotherapy in locally advanced head and neck cancer patients. Anyhow, prospective studies with different cancer types and higher number of patients are needed to validate these results.

Prediction of clinical toxicity in localized cervical carcinoma by radio-induced apoptosis study in peripheral blood lymphocytes (PBLs)

[EN] Background: Cervical cancer is treated mainly by surgery and radiotherapy. Toxicity due to radiation is a limiting factor for treatment success. Determination of lymphocyte radiosensitivity by radio-induced apoptosis arises as a possible method for predictive test development. The aim of this study was to analyze radio-induced apoptosis of peripheral blood lymphocytes. Methods: Ninety four consecutive patients suffering from cervical carcinoma, diagnosed and treated in our institution, and four healthy controls were included in the study. Toxicity was evaluated using the Lent-Soma scale. Peripheral blood lymphocytes were isolated and irradiated at 0, 1, 2 and 8 Gy during 24, 48 and 72 hours. Apoptosis was measured by flow cytometry using annexin V/propidium iodide to determine early and late apoptosis. Lymphocytes were marked with CD45 APC-conjugated monoclonal antibody. Results: Radiation-induced apoptosis (RIA) increased with radiation dose and time of incubation. Data strongly fitted to a semi logarithmic model as follows: RIA = βln(Gy) + α. This mathematical model was defined by two constants: α, is the origin of the curve in the Y axis and determines the percentage of spontaneous cell death and β, is the slope of the curve and determines the percentage of cell death induced at a determined radiation dose (β = ΔRIA/Δln(Gy)). Higher β values (increased rate of RIA at given radiation doses) were observed in patients with low sexual toxicity (Exp(B) = 0.83, C.I. 95% (0.73-0.95), p = 0.007; Exp(B) = 0.88, C.I. 95% (0.82-0.94), p = 0.001; Exp(B) = 0.93, C.I. 95% (0.88-0.99), p = 0.026 for 24, 48 and 72 hours respectively). This relation was also found with rectal (Exp(B) = 0.89, C.I. 95% (0.81-0.98), p = 0.026; Exp(B) = 0.95, C.I. 95% (0.91-0.98), p = 0.013 for 48 and 72 hours respectively) and urinary (Exp(B) = 0.83, C.I. 95% (0.71-0.97), p = 0.021 for 24 hours) toxicity. Conclusion: Radiation induced apoptosis at different time points and radiation doses fitted to a semi logarithmic model defined by a mathematical equation that gives an individual value of radiosensitivity and could predict late toxicity due to radiotherapy. Other prospective studies with higher number of patients are needed to validate these results.

Very Long Baseline Interferometry in Italy Wide-field VLBI imaging and astrometry and prospects for an Italian VLBI network including the Sardinia Radio Telescope

In this thesis the use of widefield imaging techniques and VLBI observations with a limited number of antennas are explored. I present techniques to efficiently and accurately image extremely large UV datasets. Very large VLBI datasets must be reduced into multiple, smaller datasets if today’s imaging algorithms are to be used to image them. I present a procedure for accurately shifting the phase centre of a visibility dataset. This procedure has been thoroughly tested and found to be almost two orders of magnitude more accurate than existing techniques. Errors have been found at the level of one part in 1.1 million. These are unlikely to be measurable except in the very largest UV datasets. Results of a four-station VLBI observation of a field containing multiple sources are presented. A 13 gigapixel image was constructed to search for sources across the entire primary beam of the array by generating over 700 smaller UV datasets. The source 1320+299A was detected and its astrometric position with respect to the calibrator J1329+3154 is presented. Various techniques for phase calibration and imaging across this field are explored including using the detected source as an in-beam calibrator and peeling of distant confusing sources from VLBI visibility datasets. A range of issues pertaining to wide-field VLBI have been explored including; parameterising the wide-field performance of VLBI arrays; estimating the sensitivity across the primary beam both for homogeneous and heterogeneous arrays; applying techniques such as mosaicing and primary beam correction to VLBI observations; quantifying the effects of time-average and bandwidth smearing; and calibration and imaging of wide-field VLBI datasets. The performance of a computer cluster at the Istituto di Radioastronomia in Bologna has been characterised with regard to its ability to correlate using the DiFX software correlator. Using existing software it was possible to characterise the network speed particularly for MPI applications. The capabilities of the DiFX software correlator, running on this cluster, were measured for a range of observation parameters and were shown to be commensurate with the generic performance parameters measured. The feasibility of an Italian VLBI array has been explored, with discussion of the infrastructure required, the performance of such an array, possible collaborations, and science which could be achieved. Results from a 22 GHz calibrator survey are also presented. 21 out of 33 sources were detected on a single baseline between two Italian antennas (Medicina to Noto). The results and discussions presented in this thesis suggest that wide-field VLBI is a technique whose time has finally come. Prospects for exciting new science are discussed in the final chapter.

Enhancement of Trajectory Determination of Orbiter Spacecraft by Using Pairs of Planetary Optical Images

The subject of the present thesis is about the enhancement of orbiter spacecraft navigation capabilities obtained by the standard radiometric link, taking advantage of an imaging payload and making use of a novel definition of optical measurements. An ESA Mission to Mercury called BepiColombo, was selected as a reference case for this study, and in particular its Mercury Planetary Orbiter (MPO), because of the presence of SIMBIO-SYS, an instrument suite part of the MPO payload, capable of acquiring high resolution images of the surface of Mercury. The use of optical measurements for navigation, can provide complementary informations with respect to Doppler, for enhanced performances or a relaxation of the radio tracking requisites in term of ground station schedule. Classical optical techniques based on centroids, limbs or landmarks, were the base to a novel idea for optical navigation, inspired by concepts of stereoscopic vision. In brief, the relation between two overlapped images acquired by a nadir pointed orbiter spacecraft at different times, was defined, and this information was then formulated into an optical measurement, to be processed by a navigation filter. The formulation of this novel optical observable is presented, moreover the analysis of the possible impact on the mission budget and images scheduling is addressed. Simulations are conducted using an orbit determination software already in use for spacecraft navigation in which the proposed optical measurements were implemented and the final results are given.

From Radio Channel Modeling to a System Level Perspective in Body-Centric Communications

Body-centric communications are emerging as a new paradigm in the panorama of personal communications. Being concerned with human behaviour, they are suitable for a wide variety of applications. The advances in the miniaturization of portable devices to be placed on or around the body, foster the diffusion of these systems, where the human body is the key element defining communication characteristics. This thesis investigates the human impact on body-centric communications under its distinctive aspects. First of all, the unique propagation environment defined by the body is described through a scenario-based channel modeling approach, according to the communication scenario considered, i.e., on- or on- to off-body. The novelty introduced pertains to the description of radio channel features accounting for multiple sources of variability at the same time. Secondly, the importance of a proper channel characterisation is shown integrating the on-body channel model in a system level simulator, allowing a more realistic comparison of different Physical and Medium Access Control layer solutions. Finally, the structure of a comprehensive simulation framework for system performance evaluation is proposed. It aims at merging in one tool, mobility and social features typical of the human being, together with the propagation aspects, in a scenario where multiple users interact sharing space and resources.

Breathing adapted radiotherapy: a 4D gating software for lung cancer

Purpose Physiological respiratory motion of tumors growing in the lung can be corrected with respiratory gating when treated with radiotherapy (RT). The optimal respiratory phase for beam-on may be assessed with a respiratory phase optimizer (RPO), a 4D image processing software developed with this purpose. Methods and Materials Fourteen patients with lung cancer were included in the study. Every patient underwent a 4D-CT providing ten datasets of ten phases of the respiratory cycle (0-100% of the cycle). We defined two morphological parameters for comparison of 4D-CT images in different respiratory phases: tumor-volume to lung-volume ratio and tumor-to-spinal cord distance. The RPO automatized the calculations (200 per patient) of these parameters for each phase of the respiratory cycle allowing to determine the optimal interval for RT. Results Lower lobe lung tumors not attached to the diaphragm presented with the largest motion with breathing. Maximum inspiration was considered the optimal phase for treatment in 4 patients (28.6%). In 7 patients (50%), however, the RPO showed a most favorable volumetric and spatial configuration in phases other than maximum inspiration. In 2 cases (14.4%) the RPO showed no benefit from gating. This tool was not conclusive in only one case. Conclusions The RPO software presented in this study can help to determine the optimal respiratory phase for gated RT based on a few simple morphological parameters. Easy to apply in daily routine, it may be a useful tool for selecting patients who might benefit from breathing adapted RT.

On the accuracy of Software-based Energy Estimation Techniques

This paper examines the accuracy of software-based on-line energy estimation techniques. It evaluates today’s most widespread energy estimation model in order to investigate whether the current methodology of pure software-based energy estimation running on a sensor node itself can indeed reliably and accurately determine its energy consumption - independent of the particular node instance, the traffic load the node is exposed to, or the MAC protocol the node is running. The paper enhances today’s widely used energy estimation model by integrating radio transceiver switches into the model, and proposes a methodology to find the optimal estimation model parameters. It proves by statistical validation with experimental data that the proposed model enhancement and parameter calibration methodology significantly increases the estimation accuracy.

An Active Learning Module for an Introduction to Software Engineering Course

Many schools do not begin to introduce college students to software engineering until they have had at least one semester of programming. Since software engineering is a large, complex, and abstract subject it is difficult to construct active learning exercises that build on the students’ elementary knowledge of programming and still teach basic software engineering principles. It is also the case that beginning students typically know how to construct small programs, but they have little experience with the techniques necessary to produce reliable and long-term maintainable modules. I have addressed these two concerns by defining a local standard (Montana Tech Method (MTM) Software Development Standard for Small Modules Template) that step-by-step directs students toward the construction of highly reliable small modules using well known, best-practices software engineering techniques. “Small module” is here defined as a coherent development task that can be unit tested, and can be car ried out by a single (or a pair of) software engineer(s) in at most a few weeks. The standard describes the process to be used and also provides a template for the top-level documentation. The instructional module’s sequence of mini-lectures and exercises associated with the use of this (and other) local standards are used throughout the course, which perforce covers more abstract software engineering material using traditional reading and writing assignments. The sequence of mini-lectures and hands-on assignments (many of which are done in small groups) constitutes an instructional module that can be used in any similar software engineering course.

An Architecture to offer Cloud-Based Radio Access Network as a Service

This paper addresses the novel notion of offering a radio access network as a service. Its components may be instantiated on general purpose platforms with pooled resources (both radio and hardware ones) dimensioned on-demand, elastically and following the pay-per-use principle. A novel architecture is proposed that supports this concept. The architecture's success is in its modularity, well-defined functional elements and clean separation between operational and control functions. By moving much processing traditionally located in hardware for computation in the cloud, it allows the optimisation of hardware utilization and reduction of deployment and operation costs. It enables operators to upgrade their network as well as quickly deploy and adapt resources to demand. Also, new players may easily enter the market, permitting a virtual network operator to provide connectivity to its users.

Dicto: Keeping Software Architecture Under Control

Dicto is a declarative language for specifying architectural rules using a single uniform notation. Once defined, rules can automatically be validated using adapted off-the-shelf tools.

Critical Issues of Centralized and Cloudified LTE-FDD Radio Access Networks

Cloudification of the Centralized-Radio Access Network (C-RAN) in which signal processing runs on general purpose processors inside virtual machines has lately received significant attention. Due to short deadlines in the LTE Frequency Division Duplex access method, processing time fluctuations introduced by the virtualization process have a deep impact on C-RAN performance. This paper evaluates bottlenecks of the OpenAirInterface (OAI is an open-source software-based implementation of LTE) cloud performance, provides feasibility studies on C-RAN execution, and introduces a cloud architecture that significantly reduces the encountered execution problems. In typical cloud environments, the OAI processing time deadlines cannot be guaranteed. Our proposed cloud architecture shows good characteristics for the OAI cloud execution. As an example, in our setup more than 99.5% processed LTE subframes reach reasonable processing deadlines close to performance of a dedicated machine.

Radio-holografía de microondas para la optimización de la superficie de grandes antenas reflectoras

En el presente trabajo de tesis se afronta el problema de la optimización de la superficie de grandes antenas reflectoras. Es sabido que los grandes reflectores, formados por una superficie panelada, sufren deformaciones debidas al impacto del viento, a los cambios de temperatura y a los efectos gravitacionales derivados del gran peso de la estructura. Estos efectos hacen que los reflectores pierdan su forma ideal, generalmente de paraboloide, y se reduzca su eficiencia de apertura y, por tanto, se limite la máxima frecuencia de uso de los mismos. Es necesario, por tanto, disponer de técnicas que permitan medir el estado de la superficie de grandes reflectores, y derivar los ajustes necesarios a aplicar sobre los tornillos de soporte de cada uno de los paneles que conforman dicha superficie. De esta manera, se devolvería al reflector su forma óptima y aumentaría la eficiencia de apertura y el rango de frecuencias de uso. Hay que resaltar que el aumento de la eficiencia de un radiotelescopio supone una reducción en el tiempo de integración necesario para la detección de las debilísimas señales generadas por las radiofuentes naturales, ahorrando así valioso tiempo de observación. Además, el incremento en el rango de frecuencias permite la detección de nuevas líneas o especies moleculares en dichas radiofuentes. Tras un primer capítulo introductorio, se presenta, en el capítulo segundo, la geometría de estos grandes reflectores y la influencia de los distintos factores que afectan a la calidad de la superficie de los mismos, como la gravedad, el viento y la temperatura, particularizando para el caso del radiotelescopio de 40 metros del Centro Astronómico de Yebes. En el tercer capítulo, se presentan las diferentes técnicas metrológicas empleadas actualmente para abordar la determinación de estos ajustes, mostrándose las ventajas e inconvenientes de cada una de ellas. Actualmente, la técnica metrológica más precisa y rápida para llevar a cabo esta tarea de caracterización de la superficie de un gran reflector, es la radio-holografía de microondas presentada en el capítulo cuarto. A partir de las medidas proporcionadas por esta técnica, realizadas con la ayuda de un transmisor, y mediante transformaciones de campo, se calculan los errores de la superficie del reflector, respecto al paraboloide ideal, y se derivan los ajustes necesarios. En los capítulos quinto y sexto se presentan los resultados de la aplicación de esta técnica a dos radiotelescopios: el de 30 metros de IRAM en Pico de Veleta (Granada) y los prototipos de 12 metros de las antenas del proyecto ALMA. Por su parte, el capítulo séptimo contiene el núcleo fundamental de esta tesis y presenta el desarrollo de la técnica de radio-holografía de microondas para optimizar la superficie del radiotelescopio de 40 metros del Centro Astronómico de Yebes. Para ello, ha sido necesario diseñar, construir e instalar un receptor de doble canal en banda Ku en foco primario, y la instrumentación asociada para hacer las medidas de amplitud y fase del diagrama de radiación. Además, ha sido necesario desarrollar el software para llevar a cabo las transformaciones de campo y derivar los ajustes de los paneles. De las medidas holográficas iniciales resultó un error de la superficie del radiotelescopio de 485 μm WRMS, respecto al paraboloide ideal en dirección normal. Tras varias iteraciones del proceso de medida y ajuste, se consiguió reducir dicho error a 194 μm WRMS. Esta notable mejora de la calidad de la superficie ha supuesto aumentar la eficiencia de apertura desde 2,6% al 38,2% a 86 GHz, para un receptor a esta frecuencia situado en el foco primario que produjese la misma iluminación que el receptor de holografía. In this thesis the problem of large reflector antenna surface optimization is faced. It is well known that large reflectors, which are made of a panelled surface, suffer from deformations due to the impact of wind, temperature gradients and gravity loads coming from the high weigth of the structure. These effects distort the ideal reflector shape, which is a paraboloid in most cases, hence reducing the aperture efficiency of the reflector and limiting the maximum frequency of operation. Therefore, it is necessary to have some techniques to measure the status of large reflector surfaces and to derive the adjustment values to be applied to the screws that connect the surface panels to the reflector back-up structure. In this way, the reflector would recover its optimum shape and the aperture efficiency and frequency range would increase. It has to be stated that an increment in the radiotelescope aperture efficiency would imply a reduction in the integration time needed to detect such weak signals coming from natural radiosources in space and, hence, an important saving in observation time. In addition, the increase in the frequency range of operation would allow the detection of new molecular lines in those radiosources. After the introduction, the second chapter shows the geometry of large reflector antennas and the impact on its surface quality of different factors like gravity, wind and temperature, particularly for the case of the Centro Astronómico de Yebes 40 meter radiotelescope. The third chapter deals with the different metrology techniques used to determine the panel adjustments, including the advantages and drawbacks of each one Currently, the most accurate and fast metrologic technique to carry out the characterization of large reflector surfaces is microwave radio-holography2, which is shown in chapter four. From the measurements provided by microwave radio-holography, performed with the help of a transmitter, and with the use of field transformations, the reflector surface errors are computed and the panel adjustments are derived. Chapters five and six show the results of holographic measurements applied to two first class radiotelescopes: the IRAM 30 meter radiotelescope and the 12 meter prototype antennas for the ALMA project. Chapter seven contains the main work of this thesis. It presents the development of the microwave radio-holography technique for the optimization of the Centro Astronómico de Yebes 40m radiotelescope. The work implied the design, construction and instalation of a prime focus Ku-band dual channel receiver, together with the associated instrumentation to measure the amplitude and phase of the radiotelescope radiation pattern. In addition, the software to carry out field transformations and screw settings computations was developed too. Initial holography measurements came up with an surface error of 485 μmWRMS in normal direction with respect to the best-fit paraboloid. After a few iterations of the measurementadjustment cycle, the surface error was reduced to 194 μm WRMS. This remarkable improvement in surface quality means an increment in aperture efficiency from 2,6% to 38,2% at 86 GHz, assuming a receiver at this frequency in prime focus position which produces the same illumination as the holography receiver.

Interfaz gráfica y fase de pruebas de software de vídeo forense (Sistema de codificación DV)

El presente proyecto fin de carrera, realizado por el ingeniero técnico en telecomunicaciones Pedro M. Matamala Lucas, es la fase final de desarrollo de un proyecto de mayor magnitud correspondiente al software de vídeo forense SAVID. El propósito del proyecto en su totalidad es la creación de una herramienta informática capacitada para realizar el análisis de ficheros de vídeo, codificados y comprimidos por el sistema DV –Digital Video-. El objetivo del análisis, es aportar información acerca de si la cinta magnética presenta indicios de haber sido manipulada con una edición posterior a su grabación original, además, de mostrar al usuario otros datos de interés como las especificaciones técnicas de la señal de vídeo y audio. Por lo tanto, se facilitará al usuario, analista de vídeo forense, información que le ayude a valorar la originalidad del contenido del soporte que es sujeto del análisis. El objetivo específico de esta fase final, es la creación de la interfaz de usuario del software, que informa tanto del código binario de los sectores significativos, como de su interpretación tras el análisis. También permitirá al usuario el reporte de los resultados, además de otras funcionalidades que le permitan la navegación por los sectores del código que han sido modificados como efecto colateral de la edición de la cinta magnética original. Otro objetivo importante del proyecto ha sido la investigación de metodologías y técnicas de desarrollo de software para su posterior implementación, buscando con esto, una mayor eficiencia en la gestión del tiempo y una mayor calidad de software con el fin de garantizar su evolución y sostenibilidad en el futuro. Se ha hecho hincapié en las metodologías ágiles que han ido ganando relevancia en el sector de las tecnologías de la información en las últimas décadas, sustituyendo a metodologías clásicas como el desarrollo en cascada. Su flexibilidad durante el ciclo de vida del software, permite obtener mejores resultados cuando las especificaciones no están del todo definidas, ajustándose de este modo a las condiciones del proyecto. Resumiendo las especificaciones técnicas del software, C++ es el lenguaje de programación orientado a objetos con el que se ha desarrollado, utilizándose la tecnología MFC -Microsoft Foundation Classes- para la implementación. Es un proyecto MFC de tipo cuadro de dialogo,creado, compilado y publicado, con la herramienta de desarrollo integrado Microsoft Visual Studio 2010. La arquitectura con la que se ha estructurado es la arquetípica de tres capas, compuesta por la interfaz de usuario, capa de negocio y capa de acceso a datos. Se ha visto necesario configurar el proyecto con compatibilidad con CLR –Common Languages Runtime- para poder implementar la funcionalidad de creación de reportes. Acompañando a la aplicación informática, se presenta la memoria del proyecto y sus anexos correspondientes a los documentos EDRF –Especificaciones Detalladas de Requisitos funcionales-, EIU –Especificaciones de Interfaz de Usuario , DT -Diseño Técnico- y Guía de Usuario. SUMMARY. This dissertation, carried out by the telecommunications engineer Pedro M. Matamala Lucas, is in its final stage and is part of a larger project for the software of forensic video called SAVID. The purpose of the entire project is the creation of a software tool capable of analyzing video files that are coded and compressed by the DV -Digital Video- System. The objective of the analysis is to provide information on whether the magnetic tape shows signs of having been tampered with after the editing of the original recording, and also to show the user other relevant data and technical specifications of the video signal and audio. Therefore the user, forensic video analyst, will have information to help assess the originality of the content of the media that is subject to analysis. The specific objective of this final phase is the creation of the user interface of the software that provides information about the binary code of the significant sectors and also its interpretation after analysis. It will also allow the user to report the results, and other features that will allow browsing through the sections of the code that have been modified as a secondary effect of the original magnetic tape being tampered. Another important objective of the project is the investigation of methodologies and software development techniques to be used in deployment, with the aim of greater efficiency in time management and enhanced software quality in order to ensure its development and maintenance in the future. Agile methodologies, which have become important in the field of information technology in recent decades, have been used during the execution of the project, replacing classical methodologies such as Waterfall Development. The flexibility, as the result of using by agile methodologies, during the software life cycle, produces better results when the specifications are not fully defined, thus conforming to the initial conditions of the project. Summarizing the software technical specifications, C + + the programming language – which is object oriented and has been developed using technology MFC- Microsoft Foundation Classes for implementation. It is a project type dialog box, created, compiled and released with the integrated development tool Microsoft Visual Studio 2010. The architecture is structured in three layers: the user interface, business layer and data access layer. It has been necessary to configure the project with the support CLR -Common Languages Runtime – in order to implement the reporting functionality. The software application is submitted with the project report and its annexes to the following documents: Functional Requirements Specifications - Detailed User Interface Specifications, Technical Design and User Guide.

Design and Validation of an Optimized MB-OFDM Ultra Wideband Transceiver System

Esta tesis está incluida dentro del campo del campo de Multiband Orthogonal Frequency Division Multiplexing Ultra Wideband (MB-OFDM UWB), el cual ha adquirido una gran importancia en las comunicaciones inalámbricas de alta tasa de datos en la última década. UWB surgió con el objetivo de satisfacer la creciente demanda de conexiones inalámbricas en interiores y de uso doméstico, con bajo coste y alta velocidad. La disponibilidad de un ancho de banda grande, el potencial para alta velocidad de transmisión, baja complejidad y bajo consumo de energía, unido al bajo coste de implementación, representa una oportunidad única para que UWB se convierta en una solución ampliamente utilizada en aplicaciones de Wireless Personal Area Network (WPAN). UWB está definido como cualquier transmisión que ocupa un ancho de banda de más de 20% de su frecuencia central, o más de 500 MHz. En 2002, la Comisión Federal de Comunicaciones (FCC) definió que el rango de frecuencias de transmisión de UWB legal es de 3.1 a 10.6 GHz, con una energía de transmisión de -41.3 dBm/Hz. Bajo las directrices de FCC, el uso de la tecnología UWB puede aportar una enorme capacidad en las comunicaciones de corto alcance. Considerando las ecuaciones de capacidad de Shannon, incrementar la capacidad del canal requiere un incremento lineal en el ancho de banda, mientras que un aumento similar de la capacidad de canal requiere un aumento exponencial en la energía de transmisión. En los últimos años, s diferentes desarrollos del UWB han sido extensamente estudiados en diferentes áreas, entre los cuales, el protocolo de comunicaciones inalámbricas MB-OFDM UWB está considerado como la mejor elección y ha sido adoptado como estándar ISO/IEC para los WPANs. Combinando la modulación OFDM y la transmisión de datos utilizando las técnicas de salto de frecuencia, el sistema MB-OFDM UWB es capaz de soportar tasas de datos con que pueden variar de los 55 a los 480 Mbps, alcanzando una distancia máxima de hasta 10 metros. Se esperara que la tecnología MB-OFDM tenga un consumo energético muy bajo copando un are muy reducida en silicio, proporcionando soluciones de bajo coste que satisfagan las demandas del mercado. Para cumplir con todas estas expectativas, el desarrollo y la investigación del MBOFDM UWB deben enfrentarse a varios retos, como son la sincronización de alta sensibilidad, las restricciones de baja complejidad, las estrictas limitaciones energéticas, la escalabilidad y la flexibilidad. Tales retos requieren un procesamiento digital de la señal de última generación, capaz de desarrollar sistemas que puedan aprovechar por completo las ventajas del espectro UWB y proporcionar futuras aplicaciones inalámbricas en interiores. Esta tesis se centra en la completa optimización de un sistema de transceptor de banda base MB-OFDM UWB digital, cuyo objetivo es investigar y diseñar un subsistema de comunicación inalámbrica para la aplicación de las Redes de Sensores Inalámbricas Visuales. La complejidad inherente de los procesadores FFT/IFFT y el sistema de sincronización así como la alta frecuencia de operación para todos los elementos de procesamiento, se convierten en el cuello de la botella para el diseño y la implementación del sistema de UWB digital en base de banda basado en MB-OFDM de baja energía. El objetivo del transceptor propuesto es conseguir baja energía y baja complejidad bajo la premisa de un alto rendimiento. Las optimizaciones están realizadas tanto a nivel algorítmico como a nivel arquitectural para todos los elementos del sistema. Una arquitectura hardware eficiente en consumo se propone en primer lugar para aquellos módulos correspondientes a núcleos de computación. Para el procesado de la Transformada Rápida de Fourier (FFT/IFFT), se propone un algoritmo mixed-radix, basado en una arquitectura con pipeline y se ha desarrollado un módulo de Decodificador de Viterbi (VD) equilibrado en coste-velocidad con el objetivo de reducir el consumo energético e incrementar la velocidad de procesamiento. También se ha implementado un correlador signo-bit simple basado en la sincronización del tiempo de símbolo es presentado. Este correlador es usado para detectar y sincronizar los paquetes de OFDM de forma robusta y precisa. Para el desarrollo de los subsitemas de procesamiento y realizar la integración del sistema completo se han empleado tecnologías de última generación. El dispositivo utilizado para el sistema propuesto es una FPGA Virtex 5 XC5VLX110T del fabricante Xilinx. La validación el propuesta para el sistema transceptor se ha implementado en dicha placa de FPGA. En este trabajo se presenta un algoritmo, y una arquitectura, diseñado con filosofía de co-diseño hardware/software para el desarrollo de sistemas de FPGA complejos. El objetivo principal de la estrategia propuesta es de encontrar una metodología eficiente para el diseño de un sistema de FPGA configurable optimizado con el empleo del mínimo esfuerzo posible en el sistema de procedimiento de verificación, por tanto acelerar el periodo de desarrollo del sistema. La metodología de co-diseño presentada tiene la ventaja de ser fácil de usar, contiene todos los pasos desde la propuesta del algoritmo hasta la verificación del hardware, y puede ser ampliamente extendida para casi todos los tipos de desarrollos de FPGAs. En este trabajo se ha desarrollado sólo el sistema de transceptor digital de banda base por lo que la comprobación de señales transmitidas a través del canal inalámbrico en los entornos reales de comunicación sigue requiriendo componentes RF y un front-end analógico. No obstante, utilizando la metodología de co-simulación hardware/software citada anteriormente, es posible comunicar el sistema de transmisor y el receptor digital utilizando los modelos de canales propuestos por IEEE 802.15.3a, implementados en MATLAB. Por tanto, simplemente ajustando las características de cada modelo de canal, por ejemplo, un incremento del retraso y de la frecuencia central, podemos estimar el comportamiento del sistema propuesto en diferentes escenarios y entornos. Las mayores contribuciones de esta tesis son: • Se ha propuesto un nuevo algoritmo 128-puntos base mixto FFT usando la arquitectura pipeline multi-ruta. Los complejos multiplicadores para cada etapa de procesamiento son diseñados usando la arquitectura modificada shiftadd. Los sistemas word length y twiddle word length son comparados y seleccionados basándose en la señal para cuantización del SQNR y el análisis de energías. • El desempeño del procesador IFFT es analizado bajo diferentes situaciones aritméticas de bloques de punto flotante (BFP) para el control de desbordamiento, por tanto, para encontrar la arquitectura perfecta del algoritmo IFFT basado en el procesador FFT propuesto. • Para el sistema de receptor MB-OFDM UWB se ha empleado una sincronización del tiempo innovadora, de baja complejidad y esquema de compensación, que consiste en funciones de Detector de Paquetes (PD) y Estimación del Offset del tiempo. Simplificando el cross-correlation y maximizar las funciones probables solo a sign-bit, la complejidad computacional se ve reducida significativamente. • Se ha propuesto un sistema de decodificadores Viterbi de 64 estados de decisión-débil usando velocidad base-4 de arquitectura suma-comparaselecciona. El algoritmo Two-pointer Even también es introducido en la unidad de rastreador de origen con el objetivo de conseguir la eficiencia en el hardware. • Se han integrado varias tecnologías de última generación en el completo sistema transceptor basebanda , con el objetivo de implementar un sistema de comunicación UWB altamente optimizado. • Un diseño de flujo mejorado es propuesto para el complejo sistema de implementación, el cual puede ser usado para diseños de Cadena de puertas de campo programable general (FPGA). El diseño mencionado no sólo reduce dramáticamente el tiempo para la verificación funcional, sino también provee un análisis automático como los errores del retraso del output para el sistema de hardware implementado. • Un ambiente de comunicación virtual es establecido para la validación del propuesto sistema de transceptores MB-OFDM. Este método es provisto para facilitar el uso y la conveniencia de analizar el sistema digital de basebanda sin parte frontera analógica bajo diferentes ambientes de comunicación. Esta tesis doctoral está organizada en seis capítulos. En el primer capítulo se encuentra una breve introducción al campo del UWB, tanto relacionado con el proyecto como la motivación del desarrollo del sistema de MB-OFDM. En el capítulo 2, se presenta la información general y los requisitos del protocolo de comunicación inalámbrica MBOFDM UWB. En el capítulo 3 se habla de la arquitectura del sistema de transceptor digital MB-OFDM de banda base . El diseño del algoritmo propuesto y la arquitectura para cada elemento del procesamiento está detallado en este capítulo. Los retos de diseño del sistema que involucra un compromiso de discusión entre la complejidad de diseño, el consumo de energía, el coste de hardware, el desempeño del sistema, y otros aspectos. En el capítulo 4, se ha descrito la co-diseñada metodología de hardware/software. Cada parte del flujo del diseño será detallado con algunos ejemplos que se ha hecho durante el desarrollo del sistema. Aprovechando esta estrategia de diseño, el procedimiento de comunicación virtual es llevado a cabo para probar y analizar la arquitectura del transceptor propuesto. Los resultados experimentales de la co-simulación y el informe sintético de la implementación del sistema FPGA son reflejados en el capítulo 5. Finalmente, en el capítulo 6 se incluye las conclusiones y los futuros proyectos, y también los resultados derivados de este proyecto de doctorado. ABSTRACT In recent years, the Wireless Visual Sensor Network (WVSN) has drawn great interest in wireless communication research area. They enable a wealth of new applications such as building security control, image sensing, and target localization. However, nowadays wireless communication protocols (ZigBee, Wi-Fi, and Bluetooth for example) cannot fully satisfy the demands of high data rate, low power consumption, short range, and high robustness requirements. New communication protocol is highly desired for such kind of applications. The Ultra Wideband (UWB) wireless communication protocol, which has increased in importance for high data rate wireless communication field, are emerging as an important topic for WVSN research. UWB has emerged as a technology that offers great promise to satisfy the growing demand for low-cost, high-speed digital wireless indoor and home networks. The large bandwidth available, the potential for high data rate transmission, and the potential for low complexity and low power consumption, along with low implementation cost, all present a unique opportunity for UWB to become a widely adopted radio solution for future Wireless Personal Area Network (WPAN) applications. UWB is defined as any transmission that occupies a bandwidth of more than 20% of its center frequency, or more than 500 MHz. In 2002, the Federal Communications Commission (FCC) has mandated that UWB radio transmission can legally operate in the range from 3.1 to 10.6 GHz at a transmitter power of －41.3 dBm/Hz. Under the FCC guidelines, the use of UWB technology can provide enormous capacity over short communication ranges. Considering Shannon’s capacity equations, increasing the channel capacity requires linear increasing in bandwidth, whereas similar channel capacity increases would require exponential increases in transmission power. In recent years, several different UWB developments has been widely studied in different area, among which, the MB-OFDM UWB wireless communication protocol is considered to be the leading choice and has recently been adopted in the ISO/IEC standard for WPANs. By combing the OFDM modulation and data transmission using frequency hopping techniques, the MB-OFDM UWB system is able to support various data rates, ranging from 55 to 480 Mbps, over distances up to 10 meters. The MB-OFDM technology is expected to consume very little power and silicon area, as well as provide low-cost solutions that can satisfy consumer market demands. To fulfill these expectations, MB-OFDM UWB research and development have to cope with several challenges, which consist of high-sensitivity synchronization, low- complexity constraints, strict power limitations, scalability, and flexibility. Such challenges require state-of-the-art digital signal processing expertise to develop systems that could fully take advantages of the UWB spectrum and support future indoor wireless applications. This thesis focuses on fully optimization for the MB-OFDM UWB digital baseband transceiver system, aiming at researching and designing a wireless communication subsystem for the Wireless Visual Sensor Networks (WVSNs) application. The inherent high complexity of the FFT/IFFT processor and synchronization system, and high operation frequency for all processing elements, becomes the bottleneck for low power MB-OFDM based UWB digital baseband system hardware design and implementation. The proposed transceiver system targets low power and low complexity under the premise of high performance. Optimizations are made at both algorithm and architecture level for each element of the transceiver system. The low-power hardwareefficient structures are firstly proposed for those core computation modules, i.e., the mixed-radix algorithm based pipelined architecture is proposed for the Fast Fourier Transform (FFT/IFFT) processor, and the cost-speed balanced Viterbi Decoder (VD) module is developed, in the aim of lowering the power consumption and increasing the processing speed. In addition, a low complexity sign-bit correlation based symbol timing synchronization scheme is presented so as to detect and synchronize the OFDM packets robustly and accurately. Moreover, several state-of-the-art technologies are used for developing other processing subsystems and an entire MB-OFDM digital baseband transceiver system is integrated. The target device for the proposed transceiver system is Xilinx Virtex 5 XC5VLX110T FPGA board. In order to validate the proposed transceiver system in the FPGA board, a unified algorithm-architecture-circuit hardware/software co-design environment for complex FPGA system development is presented in this work. The main objective of the proposed strategy is to find an efficient methodology for designing a configurable optimized FPGA system by using as few efforts as possible in system verification procedure, so as to speed up the system development period. The presented co-design methodology has the advantages of easy to use, covering all steps from algorithm proposal to hardware verification, and widely spread for almost all kinds of FPGA developments. Because only the digital baseband transceiver system is developed in this thesis, the validation of transmitting signals through wireless channel in real communication environments still requires the analog front-end and RF components. However, by using the aforementioned hardware/software co-simulation methodology, the transmitter and receiver digital baseband systems get the opportunity to communicate with each other through the channel models, which are proposed from the IEEE 802.15.3a research group, established in MATLAB. Thus, by simply adjust the characteristics of each channel model, e.g. mean excess delay and center frequency, we can estimate the transmission performance of the proposed transceiver system through different communication situations. The main contributions of this thesis are: • A novel mixed radix 128-point FFT algorithm by using multipath pipelined architecture is proposed. The complex multipliers for each processing stage are designed by using modified shift-add architectures. The system wordlength and twiddle word-length are compared and selected based on Signal to Quantization Noise Ratio (SQNR) and power analysis. • IFFT processor performance is analyzed under different Block Floating Point (BFP) arithmetic situations for overflow control, so as to find out the perfect architecture of IFFT algorithm based on the proposed FFT processor. • An innovative low complex timing synchronization and compensation scheme, which consists of Packet Detector (PD) and Timing Offset Estimation (TOE) functions, for MB-OFDM UWB receiver system is employed. By simplifying the cross-correlation and maximum likelihood functions to signbit only, the computational complexity is significantly reduced. • A 64 state soft-decision Viterbi Decoder system by using high speed radix-4 Add-Compare-Select architecture is proposed. Two-pointer Even algorithm is also introduced into the Trace Back unit in the aim of hardware-efficiency. • Several state-of-the-art technologies are integrated into the complete baseband transceiver system, in the aim of implementing a highly-optimized UWB communication system. • An improved design flow is proposed for complex system implementation which can be used for general Field-Programmable Gate Array (FPGA) designs. The design method not only dramatically reduces the time for functional verification, but also provides automatic analysis such as errors and output delays for the implemented hardware systems. • A virtual communication environment is established for validating the proposed MB-OFDM transceiver system. This methodology is proved to be easy for usage and convenient for analyzing the digital baseband system without analog frontend under different communication environments. This PhD thesis is organized in six chapters. In the chapter 1 a brief introduction to the UWB field, as well as the related work, is done, along with the motivation of MBOFDM system development. In the chapter 2, the general information and requirement of MB-OFDM UWB wireless communication protocol is presented. In the chapter 3, the architecture of the MB-OFDM digital baseband transceiver system is presented. The design of the proposed algorithm and architecture for each processing element is detailed in this chapter. Design challenges of such system involve trade-off discussions among design complexity, power consumption, hardware cost, system performance, and some other aspects. All these factors are analyzed and discussed. In the chapter 4, the hardware/software co-design methodology is proposed. Each step of this design flow will be detailed by taking some examples that we met during system development. Then, taking advantages of this design strategy, the Virtual Communication procedure is carried out so as to test and analyze the proposed transceiver architecture. Experimental results from the co-simulation and synthesis report of the implemented FPGA system are given in the chapter 5. The chapter 6 includes conclusions and future work, as well as the results derived from this PhD work.