Replication Data Management,needs and solutions: an initial evaluation of conceptual approaches for integrating heterogeneous replication study data

Replication Data Management (RDM) aims at enabling the use of data collections from several iterations of an experiment. However, there are several major challenges to RDM from integrating data models and data from empirical study infrastructures that were not designed to cooperate, e.g., data model variation of local data sources. [Objective] In this paper we analyze RDM needs and evaluate conceptual RDM approaches to support replication researchers. [Method] We adapted the ATAM evaluation process to (a) analyze RDM use cases and needs of empirical replication study research groups and (b) compare three conceptual approaches to address these RDM needs: central data repositories with a fixed data model, heterogeneous local repositories, and an empirical ecosystem. [Results] While the central and local approaches have major issues that are hard to resolve in practice, the empirical ecosystem allows bridging current gaps in RDM from heterogeneous data sources. [Conclusions] The empirical ecosystem approach should be explored in diverse empirical environments.

Aprendizaje, simulación y desarrollo sobre las tecnologías de voz y datos

El objetivo del Proyecto Fin de Carrera (PFC) es el de conocer, simular y crear una red VoIP sobre una red de datos en un entorno docente, más concretamente, en la asignatura Redes y Servicios de telecomunicación en Grado en Ingeniería de Telecomunicaciones en la Universidad Politécnica de Madrid (UPM). Una vez se adquieran los conocimientos necesarios, se propondrán una serie de prácticas para que los alumnos se vayan familiarizando con el software y hardware utilizados, de manera que, se irá subiendo el grado de dificultad hasta que puedan realizar una auténtica red VoIP por sí mismos. A parte de la realización de las prácticas, los alumnos deberán pasar una prueba de los conocimientos adquiridos al final de cada práctica mediante preguntas tipo test. Los sistemas elegidos para la implantación de una red VoIP en los módulos de laboratorio son: 3CX System Phone y Asteisk-Trixbox. Los cuales, son capaces de trabajar mediante gestores gráficos para simplificar el nivel de dificultad de la configuración. 3CX es una PBX que trabaja sobre Windows y se basa exclusivamente en el protocolo SIP. Esto facilita el manejo para usuarios que solo han usado Windows sin quitar funcionalidades que tienen otras centralitas en otros sistemas operativos. La versión demo activa todas las opciones para poder familiarizarse con este sistema. Por otro lado, Asterisk trabaja en todas las plataformas, aunque se ha seleccionado trabajar sobre Linux. Esta selección se ha realizado porque el resto de plataformas limitan la configuración de la IP PBX, esta es de código abierto y permite realizar todo tipo de configuraciones. Además, es un software gratuito, esto es una ventaja a la hora de configurar novedades o resolver problemas, ya que hay muchos especialistas que dan soporte y ayudan de forma gratuita. La voz sobre Internet es habitualmente conocida como VoIP (Voice Over IP), debido a que IP (Internet Protocol) es el protocolo de red de Internet. Como tecnología, la VoIP no es solo un paso más en el crecimiento de las comunicaciones por voz, sino que supone integrar las comunicaciones de datos y las de voz en una misma red, y en concreto, en la red con mayor cobertura mundial: Internet. La mayor importancia y motivación de este Proyecto Fin de Carrera es que el alumno sea capaz de llegar a un entorno laboral y pueda tener unos conocimientos capaces de afrontar esta tecnología que esta tan a la orden del día. La importancia que estas redes tienen y tendrán en un futuro muy próximo en el mundo de la informática y las comunicaciones. Cabe decir, que se observa que estas disciplinas tecnológicas evolucionan a pasos agigantados y se requieren conocimientos más sólidos. ABSTRACT. The objective of my final project during my studies in university was, to simulate and create a VoIP network over a data network in a teaching environment, more specifically on the subject of telecommunications networks and services in Telecommunication Engineering Degree in Polytechnic University of Madrid (UPM). Once acquiring the necessary knowledge a number of practices were proposed to the students to become familiar with the software and hardware used, so that it would rise to the level of difficulty that they could make a real VoIP network for themselves. Parts of the experimental practices were that students must pass a test of knowledge acquired at the end of each practice by choice questions. The systems chosen for the implementation of a VoIP network in the laboratory modules are: 3CX Phone System and Asteisk - Trixbox. Which were able to work with graphics operators to simplify the difficulty level of the configuration. 3CX is a PBX that works on Windows and is based solely on the SIP protocol. This facilitates handling for users who have only used Windows without removing functionality with other exchanges in other operating systems. Active demo version all options to get to grips with this system. Moreover, Asterisk works on all platforms, but has been selected to work on Linux. This selection was made because other platforms limit the IP PBX configuration, as this is open source and allows all kinds of configurations. Also, Linux is a free software and an advantage when configuring new or solve problems, as there are many specialists that support and help for free. Voice over Internet is commonly known as VoIP (Voice Over IP), because IP (Internet Protocol) is the Internet protocol network. As technology, VoIP is not just another step in the growth of voice communications, but communications of integrating data and voice on a single network, and in particular, in the network with the largest global coverage: Internet. The increased importance and motivation of this Thesis is that the student is able to reach a working environment and may have some knowledge to deal with these technologies that is so much the order of the day. The importances of these networks have and will be of essences in the very near future in the world of computing and communications. It must be said it is observed that these technological disciplines evolve by leaps and bounds stronger knowledge required.

Recuperación cruzada de información pública clínico-genómica a partir de consultas sobre repositorios clínicos privados

Parte de la investigación biomédica actual se encuentra centrada en el análisis de datos heterogéneos. Estos datos pueden tener distinto origen, estructura, y semántica. Gran cantidad de datos de interés para los investigadores se encuentran en bases de datos públicas, que recogen información de distintas fuentes y la ponen a disposición de la comunidad de forma gratuita. Para homogeneizar estas fuentes de datos públicas con otras de origen privado, existen diversas herramientas y técnicas que permiten automatizar los procesos de homogeneización de datos heterogéneos. El Grupo de Informática Biomédica (GIB) [1] de la Universidad Politécnica de Madrid colabora en el proyecto europeo P-medicine [2], cuya finalidad reside en el desarrollo de una infraestructura que facilite la evolución de los procedimientos médicos actuales hacia la medicina personalizada. Una de las tareas enmarcadas en el proyecto P-medicine que tiene asignado el grupo consiste en elaborar herramientas que ayuden a usuarios en el proceso de integración de datos contenidos en fuentes de información heterogéneas. Algunas de estas fuentes de información son bases de datos públicas de ámbito biomédico contenidas en la plataforma NCBI [3] (National Center for Biotechnology Information). Una de las herramientas que el grupo desarrolla para integrar fuentes de datos es Ontology Annotator. En una de sus fases, la labor del usuario consiste en recuperar información de una base de datos pública y seleccionar de forma manual los resultados relevantes. Para automatizar el proceso de búsqueda y selección de resultados relevantes, por un lado existe un gran interés en conseguir generar consultas que guíen hacia resultados lo más precisos y exactos como sea posible, por otro lado, existe un gran interés en extraer información relevante de elevadas cantidades de documentos, lo cual requiere de sistemas que analicen y ponderen los datos que caracterizan a los mismos. En el campo informático de la inteligencia artificial, dentro de la rama de la recuperación de la información, existen diversos estudios acerca de la expansión de consultas a partir de retroalimentación relevante que podrían ser de gran utilidad para dar solución a la cuestión. Estos estudios se centran en técnicas para reformular o expandir la consulta inicial utilizando como realimentación los resultados que en una primera instancia fueron relevantes para el usuario, de forma que el nuevo conjunto de resultados tenga mayor proximidad con los que el usuario realmente desea. El objetivo de este trabajo de fin de grado consiste en el estudio, implementación y experimentación de métodos que automaticen el proceso de extracción de información trascendente de documentos, utilizándola para expandir o reformular consultas. De esta forma se pretende mejorar la precisión y el ranking de los resultados asociados. Dichos métodos serán integrados en la herramienta Ontology Annotator y enfocados a la fuente de datos de PubMed [4].---ABSTRACT---Part of the current biomedical research is focused on the analysis of heterogeneous data. These data may have different origin, structure and semantics. A big quantity of interesting data is contained in public databases which gather information from different sources and make it open and free to be used by the community. In order to homogenize thise sources of public data with others which origin is private, there are some tools and techniques that allow automating the processes of integration heterogeneous data. The biomedical informatics group of the Universidad Politécnica de Madrid cooperates with the European project P-medicine which main purpose is to create an infrastructure and models to facilitate the transition from current medical practice to personalized medicine. One of the tasks of the project that the group is in charge of consists on the development of tools that will help users in the process of integrating data from diverse sources. Some of the sources are biomedical public data bases from the NCBI platform (National Center for Biotechnology Information). One of the tools in which the group is currently working on for the integration of data sources is called the Ontology Annotator. In this tool there is a phase in which the user has to retrieve information from a public data base and select the relevant data contained in it manually. For automating the process of searching and selecting data on the one hand, there is an interest in automatically generating queries that guide towards the more precise results as possible. On the other hand, there is an interest on retrieve relevant information from large quantities of documents. The solution requires systems that analyze and weigh the data allowing the localization of the relevant items. In the computer science field of the artificial intelligence, in the branch of information retrieval there are diverse studies about the query expansion from relevance feedback that could be used to solve the problem. The main purpose of this studies is to obtain a set of results that is the closer as possible to the information that the user really wants to retrieve. In order to reach this purpose different techniques are used to reformulate or expand the initial query using a feedback the results that where relevant for the user, with this method, the new set of results will have more proximity with the ones that the user really desires. The goal of this final dissertation project consists on the study, implementation and experimentation of methods that automate the process of extraction of relevant information from documents using this information to expand queries. This way, the precision and the ranking of the results associated will be improved. These methods will be integrated in the Ontology Annotator tool and will focus on the PubMed data source.

Showing the Past: Integrating Cartographic Collections through Virtual Map Rooms

Spatial Data Infrastructures have become a methodological and technological benchmark enabling distributed access to historical-cartographic archives. However, it is essential to offer enhanced virtual tools that imitate the current processes and methodologies that are carried out by librarians, historians and academics in the existing map libraries around the world. These virtual processes must be supported by a generic framework for managing, querying, and accessing distributed georeferenced resources and other content types such as scientific data or information. The authors have designed and developed support tools to provide enriched browsing, measurement and geometrical analysis capabilities, and dynamical querying methods, based on SDI foundations. The DIGMAP engine and the IBERCARTO collection enable access to georeferenced historical-cartographical archives. Based on lessons learned from the CartoVIRTUAL and DynCoopNet projects, a generic service architecture scheme is proposed. This way, it is possible to achieve the integration of virtual map rooms and SDI technologies bringing support to researchers within the historical and social domains.

Integrating software testing and run-time checking in an assertion verification framework

We have designed and implemented a framework that unifies unit testing and run-time verification (as well as static verification and static debugging). A key contribution of our approach is that a unified assertion language is used for all of these tasks. We first propose methods for compiling runtime checks for (parts of) assertions which cannot be verified at compile-time via program transformation. This transformation allows checking preconditions and postconditions, including conditional postconditions, properties at arbitrary program points, and certain computational properties. The implemented transformation includes several optimizations to reduce run-time overhead. We also propose a minimal addition to the assertion language which allows defining unit tests to be run in order to detect possible violations of the (partial) specifications expressed by the assertions. This language can express for example the input data for performing the unit tests or the number of times that the unit tests should be repeated. We have implemented the framework within the Ciao/CiaoPP system and effectively applied it to the verification of ISO-prolog compliance and to the detection of different types of bugs in the Ciao system source code. Several experimental results are presented that ¡Ilústrate different trade-offs among program size, running time, or levéis of verbosity of the messages shown to the user.

Integrating software testing and run-time checking in an assertion verification framework.

We have designed and implemented a framework that unifies unit testing and run-time verification (as well as static verification and static debugging). A key contribution of our approach is that a unified assertion language is used for all of these tasks. We first propose methods for compiling runtime checks for (parts of) assertions which cannot be verified at compile-time via program transformation. This transformation allows checking preconditions and postconditions, including conditional postconditions, properties at arbitrary program points, and certain computational properties. The implemented transformation includes several optimizations to reduce run-time overhead. We also propose a minimal addition to the assertion language which allows defining unit tests to be run in order to detect possible violations of the (partial) specifications expressed by the assertions. This language can express for example the input data for performing the unit tests or the number of times that the unit tests should be repeated. We have implemented the framework within the Ciao/CiaoPP system and effectively applied it to the verification of ISO-prolog compliance and to the detection of different types of bugs in the Ciao system source code. Several experimental results are presented that illustrate different trade-offs among program size, running time, or levels of verbosity of the messages shown to the user.

Integrating WordNet and Wiktionary with lemon

Nowadays, there is a significant quantity of linguistic data available on the Web. However, linguistic resources are often published using proprietary formats and, as such, it can be difficult to interface with one another and they end up confined in “data silos”. The creation of web standards for the publishing of data on the Web and projects to create Linked Data have lead to interest in the creation of resources that can be published using Web principles. One of the most important aspects of “Lexical Linked Data” is the sharing of lexica and machine readable dictionaries. It is for this reason, that the lemon format has been proposed, which we briefly describe. We then consider two resources that seem ideal candidates for the Linked Data cloud, namely WordNet 3.0 and Wiktionary, a large document based dictionary. We discuss the challenges of converting both resources to lemon , and in particular for Wiktionary, the challenge of processing the mark-up, and handling inconsistencies and underspecification in the source material. Finally, we turn to the task of creating links between the two resources and present a novel algorithm for linking lexica as lexical Linked Data.

Brain tissue segmentation on Diffusion Weighted Magnetic Resonance data

Introduction Diffusion weighted Imaging (DWI) techniques are able to measure, in vivo and non-invasively, the diffusivity of water molecules inside the human brain. DWI has been applied on cerebral ischemia, brain maturation, epilepsy, multiple sclerosis, etc. [1]. Nowadays, there is a very high availability of these images. DWI allows the identification of brain tissues, so its accurate segmentation is a common initial step for the referred applications. Materials and Methods We present a validation study on automated segmentation of DWI based on the Gaussian mixture and hidden Markov random field models. This methodology is widely solved with iterative conditional modes algorithm, but some studies suggest [2] that graph-cuts (GC) algorithms improve the results when initialization is not close to the final solution. We implemented a segmentation tool integrating ITK with a GC algorithm [3], and a validation software using fuzzy overlap measures [4]. Results Segmentation accuracy of each tool is tested against a gold-standard segmentation obtained from a T1 MPRAGE magnetic resonance image of the same subject, registered to the DWI space. The proposed software shows meaningful improvements by using the GC energy minimization approach on DTI and DSI (Diffusion Spectrum Imaging) data. Conclusions The brain tissues segmentation on DWI is a fundamental step on many applications. Accuracy and robustness improvements are achieved with the proposed software, with high impact on the application’s final result.

Integrating geographical information in the Linked Digital Earth

Many progresses have been made since the Digital Earth notion was envisioned thirteen years ago. However, the mechanism for integrating geographic information into the Digital Earth is still quite limited. In this context, we have developed a process to generate, integrate and publish geospatial Linked Data from several Spanish National data-sets. These data-sets are related to four Infrastructure for Spatial Information in the European Community (INSPIRE) themes, specifically with Administrative units, Hydrography, Statistical units, and Meteorology. Our main goal is to combine different sources (heterogeneous, multidisciplinary, multitemporal, multiresolution, and multilingual) using Linked Data principles. This goal allows the overcoming of current problems of information integration and driving geographical information toward the next decade scenario, that is, ?Linked Digital Earth.?

A linked data approach to sentiment and emotion analysis of twitter in the financial domain

Sentiment analysis has recently gained popularity in the financial domain thanks to its capability to predict the stock market based on the wisdom of the crowds. Nevertheless, current sentiment indicators are still silos that cannot be combined to get better insight about the mood of different communities. In this article we propose a Linked Data approach for modelling sentiment and emotions about financial entities. We aim at integrating sentiment information from different communities or providers, and complements existing initiatives such as FIBO. The ap- proach has been validated in the semantic annotation of tweets of several stocks in the Spanish stock market, including its sentiment information.