Enhanced reproducibility of SADI web service workflows with Galaxy and Docke

Background: Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. Findings: This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. Conclusions: The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.

DBpedia spotlight: shedding light on the web of documents

Interlinking text documents with Linked Open Data enables the Web of Data to be used as background knowledge within document-oriented applications such as search and faceted browsing. As a step towards interconnecting the Web of Documents with the Web of Data, we developed DBpedia Spotlight, a system for automatically annotating text documents with DBpedia URIs. DBpedia Spotlight allows users to congure the annotations to their specic needs through the DBpedia Ontology and quality measures such as prominence, topical pertinence, contextual ambiguity and disambiguation condence. We compare our approach with the state of the art in disambiguation, and evaluate our results in light of three baselines and six publicly available annotation systems, demonstrating the competitiveness of our system. DBpedia Spotlight is shared as open source and deployed as a Web Service freely available for public use.

DBpedia Spotlight: Shedding Light on the Web of Documents

Interlinking text documents with Linked Open Data enables the Web of Data to be used as background knowledge within document-oriented applications such as search and faceted browsing. As a step towards interconnecting the Web of Documents with the Web of Data, we developed DBpedia Spotlight, a system for automatically annotating text documents with DBpedia URIs. DBpedia Spotlight allows users to configure the annotations to their specific needs through the DBpedia Ontology and quality measures such as prominence, topical pertinence, contextual ambiguity and disambiguation confidence. We compare our approach with the state of the art in disambiguation, and evaluate our results in light of three baselines and six publicly available annotation systems, demonstrating the competitiveness of our system. DBpedia Spotlight is shared as open source and deployed as a Web Service freely available for public use.

Towards data-aware cost-driven adaptation for service orchestrations.

Several activities in service oriented computing, such as automatic composition, monitoring, and adaptation, can benefit from knowing properties of a given service composition before executing them. Among these properties we will focus on those related to execution cost and resource usage, in a wide sense, as they can be linked to QoS characteristics. In order to attain more accuracy, we formulate execution costs / resource usage as functions on input data (or appropriate abstractions thereof) and show how these functions can be used to make better, more informed decisions when performing composition, adaptation, and proactive monitoring. We present an approach to, on one hand, synthesizing these functions in an automatic fashion from the definition of the different orchestrations taking part in a system and, on the other hand, to effectively using them to reduce the overall costs of non-trivial service-based systems featuring sensitivity to data and possibility of failure. We validate our approach by means of simulations of scenarios needing runtime selection of services and adaptation due to service failure. A number of rebinding strategies, including the use of cost functions, are compared.

Towards data-aware resource analysis for service orchestrations

Compile-time program analysis techniques can be applied to Web service orchestrations to prove or check various properties. In particular, service orchestrations can be subjected to resource analysis, in which safe approximations of upper and lower resource usage bounds are deduced. A uniform analysis can be simultaneously performed for different generalized resources that can be directiy correlated with cost- and performance-related quality attributes, such as invocations of partners, network traffic, number of activities, iterations, and data accesses. The resulting safe upper and lower bounds do not depend on probabilistic assumptions, and are expressed as functions of size or length of data components from an initiating message, using a finegrained structured data model that corresponds to the XML-style of information structuring. The analysis is performed by transforming a BPEL-like representation of an orchestration into an equivalent program in another programming language for which the appropriate analysis tools already exist.

Constraint-based runtime prediction of SLA violations in service orchestrations

Service compositions put together loosely-coupled component services to perform more complex, higher level, or cross-organizational tasks in a platform-independent manner. Quality-of-Service (QoS) properties, such as execution time, availability, or cost, are critical for their usability, and permissible boundaries for their values are defined in Service Level Agreements (SLAs). We propose a method whereby constraints that model SLA conformance and violation are derived at any given point of the execution of a service composition. These constraints are generated using the structure of the composition and properties of the component services, which can be either known or empirically measured. Violation of these constraints means that the corresponding scenario is unfeasible, while satisfaction gives values for the constrained variables (start / end times for activities, or number of loop iterations) which make the scenario possible. These results can be used to perform optimized service matching or trigger preventive adaptation or healing.

Servicio Web para gestión de juego cooperativo sobre desarrollo humano

Este Proyecto Fin de Carrera (PFC) tiene como objetivos el análisis, diseño e implementación de un sistema web que permita a los usuarios familiarizarse con el Índice de Desarrollo Humano (IDH), publicado anualmente por Naciones Unidas, ofreciendo un servicio de gestión y descarga de una aplicación móvil relacionada con dicho índice. La aplicación móvil es un juego educativo basado en preguntas sobre el IDH de los países, desarrollada en paralelo con este proyecto. El servicio web implementado en este proyecto facilita tanto la descarga, administración y actualización de contenidos como la interacción entre los usuarios. El sistema está formado por un servidor web, una base de datos de usuarios y contenidos y un portal web desde el cual puede descargarse la aplicación móvil, realizar consultas sobre estadísticas de juego y conocer el IDH sin necesidad de jugar. El buscador avanzado que ha sido desarrollado para conocer el IDH permite al usuario adquirir destrezas y entrenarse por sí solo para mejorar sus resultados de juego. Los administradores del sistema tienen la capacidad de gestionar el contenido del portal, los usuarios que solicitan darse de alta y la funcionalidad ofrecida, es decir, actualización del juego, foros y noticias. La instalación del sistema implementado en un servidor web ha permitido su verificación exitosa así como la provisión del servicio de información y sensibilización sobre el IDH, actualizado mediante la información de Naciones Unidas, motivación original del proyecto. ABSTRACT This Final Year Project takes as targets the analysis, design and implementation of a web system that allows to the users to familiarize with the Human Development Index (HDI), published annually by United Nations, offering a service of management and download a mobile application associated with that index. The mobile application is an educational game based on questions on the IDH of the countries, developed in parallel with this project. The web service implemented by means of this Project facilitates download, administration and update of contents and the interaction between the users across the cooperative game. The system consists of a web server, a database of users and content and a web portal from which you can download the mobile application, perform queries on game statistics, or discover the HDI without need for play. The advanced search engine that has been developed for the HDI allows the user to purchase and train for skills to improve their game results. System administrators have the ability to manage the content of the portal, users requesting register and the functionality offered, i.e., update to the game, forums and news. The installation of the system that was implemented has allowed successful verification and the provision of an information and awareness on the HDI, updated with the information from the United Nations, original motivation of the project.

Virtualización de dispositivos para servicios en la Ciudad del Futuro

El aumento de las capacidades de interconexión de dispositivos de todo tipo está suponiendo una revolución en el campo de la prestación de servicios, tanto en la cantidad como en la variedad. Esta evolución ha puesto de manifiesto la necesidad de abordar un desarrollo tecnológico sin precedentes, donde la previsión de dispositivos interconectados e interoperando entre sí y con las personas alcanza cifras del orden de los millardos. Esta idea de un mundo de cosas interconectadas ha dado lugar a una visión que se ha dado en llamar Internet de las Cosas. Un mundo donde las cosas de cualquier tipo pueden interactuar con otras cosas, incluyendo las que forman parte de redes con recurso limitados. Y esto además conduce a la creación de servicios compuestos que superan a la suma de las partes. Además de la relevancia tecnológica, esta nueva visión enlaza con la de la Ciudad del Futuro. Un concepto que recurre a la convergencia de la energía, el transporte y las tecnologías de la información y las comunicaciones para definir una forma mediante la que lograr el crecimiento sostenible y competitivo, mejorando así la calidad de vida y abriendo el gobierno de las ciudades a la participación ciudadana. En la línea de desarrollo que permite avanzar hacia la consecución de tales objetivos, este Proyecto Fin de Carrera propone una forma de virtualizar los servicios ofrecidos por la diversidad de dispositivos que van adquiriendo la capacidad de interoperar en una red. Para ello se apoya en el uso de una capa de intermediación orientada a servicios, nSOM, desarrollada en la EUITT. Sobre esta arquitectura se proponen como objetivos el diseño y desarrollo de una pasarela de servicios que haga accesibles desde la web los recursos ofrecidos en una red de sensores; el diseño y desarrollo de un registro de dispositivos y servicios en concordancia a la propuesta de arquitectura de referencia para Internet de las Cosas; y el estudio y diseño de un marco para la composición de servicios orquestados en redes de recursos limitados. Para alcanzar estos objetivos primero se abordará un estudio del estado del arte donde se profundizará en el conocimiento de la las tecnologías para la interoperatividad entre cosas, abordando los principios de las redes inalámbricas de sensores y actuadores, las arquitecturas para las comunicaciones Máquina a Máquina e Internet de las Cosas, y la visión de la Web de las Cosas. Seguidamente se tratarán las tecnologías de red y de servicios de interés, para finalizar con un breve repaso a las tecnologías para la composición de servicios. Le seguirá una descripción detallada de la arquitectura nSOM y del diseño propuesto para este proyecto. Finalmente se propondrá un escenario sobre el que se llevarán a cabo diferentes pruebas de validación. ABSTRACT. The increasing of the capabilities of all kind of devices is causing a revolution in the field of the provision of services, both in quantity and in diversity. This situation has highlighted the need to address unprecedented technological development, where the forecast of interconnected and interoperable devices between them and human beings reaches the order of billions. And these numbers go further when the connectivity of constrained networks is taken into account. This idea of an interconnected world of things has led to a vision that has been called "The Internet of Things". It’s a vision of a world where things of any kind can interact with other things, even those in the domain of a constrained network. This also leads to the creation of new composed services that exceed the sum of the parts. Besides the technological interest, this new vision relates with the one from the Smart City. A concept that uses the convergence of the energy, the transport, and the information and communication technologies to define a way to achieve sustainable and competitive growth, improving the quality of life, and opening the governance of the cities to the participation. In the development pathway to reach these goals, this Final Degree Dissertation proposes a way for the virtualization of the services offered by the variety of devices that are reaching the ability to interoperate in a network. For this it is supported by a service oriented middleware called nSOM that has been developed at EUITT. Using this architecture the goals proposed for this project are the design and development of a service gateway that makes available the resources of a sensor network through a web interface; the design and development of a Device & Service Registry according to the reference architecture proposal for the Internet of Things; and the study and design of a composition framework for orchestrated services in constrained networks. To achieve these goals this dissertation begins with a State of the Art study where the background knowledge about the technologies in use for the interoperation of things will be settled. At first it starts talking about Wireless Sensor and Actuator Networks, the architectures for Machine-to-Machine communication and Internet of Things, and also the concepts for the Web of Things vision. Next the related network and services technologies are explored, ending with a brief review of service composition technologies. Then will follow a detailed description of the nSOM architecture, and also of the proposed design for this project. Finally a scenario will be proposed where a series of validation tests will be conducted.

A Coreference Service for Enterprise Application Integration using Linked Data

The use of semantic and Linked Data technologies for Enterprise Application Integration (EAI) is increasing in recent years. Linked Data and Semantic Web technologies such as the Resource Description Framework (RDF) data model provide several key advantages over the current de-facto Web Service and XML based integration approaches. The flexibility provided by representing the data in a more versatile RDF model using ontologies enables avoiding complex schema transformations and makes data more accessible using Web standards, preventing the formation of data silos. These three benefits represent an edge for Linked Data-based EAI. However, work still has to be performed so that these technologies can cope with the particularities of the EAI scenarios in different terms, such as data control, ownership, consistency, or accuracy. The first part of the paper provides an introduction to Enterprise Application Integration using Linked Data and the requirements imposed by EAI to Linked Data technologies focusing on one of the problems that arise in this scenario, the coreference problem, and presents a coreference service that supports the use of Linked Data in EAI systems. The proposed solution introduces the use of a context that aggregates a set of related identities and mappings from the identities to different resources that reside in distinct applications and provide different views or aspects of the same entity. A detailed architecture of the Coreference Service is presented explaining how it can be used to manage the contexts, identities, resources, and applications which they relate to. The paper shows how the proposed service can be utilized in an EAI scenario using an example involving a dashboard that integrates data from different systems and the proposed workflow for registering and resolving identities. As most enterprise applications are driven by business processes and involve legacy data, the proposed approach can be easily incorporated into enterprise applications.

Analysis of service-oriented computing systems

La computación basada en servicios (Service-Oriented Computing, SOC) se estableció como un paradigma ampliamente aceptado para el desarollo de sistemas de software flexibles, distribuidos y adaptables, donde las composiciones de los servicios realizan las tareas más complejas o de nivel más alto, frecuentemente tareas inter-organizativas usando los servicios atómicos u otras composiciones de servicios. En tales sistemas, las propriedades de la calidad de servicio (Quality of Service, QoS), como la rapídez de procesamiento, coste, disponibilidad o seguridad, son críticas para la usabilidad de los servicios o sus composiciones en cualquier aplicación concreta. El análisis de estas propriedades se puede realizarse de una forma más precisa y rica en información si se utilizan las técnicas de análisis de programas, como el análisis de complejidad o de compartición de datos, que son capables de analizar simultáneamente tanto las estructuras de control como las de datos, dependencias y operaciones en una composición. El análisis de coste computacional para la composicion de servicios puede ayudar a una monitorización predictiva así como a una adaptación proactiva a través de una inferencia automática de coste computacional, usando los limites altos y bajos como funciones del valor o del tamaño de los mensajes de entrada. Tales funciones de coste se pueden usar para adaptación en la forma de selección de los candidatos entre los servicios que minimizan el coste total de la composición, basado en los datos reales que se pasan al servicio. Las funciones de coste también pueden ser combinadas con los parámetros extraídos empíricamente desde la infraestructura, para producir las funciones de los límites de QoS sobre los datos de entrada, cuales se pueden usar para previsar, en el momento de invocación, las violaciones de los compromisos al nivel de servicios (Service Level Agreements, SLA) potenciales or inminentes. En las composiciones críticas, una previsión continua de QoS bastante eficaz y precisa se puede basar en el modelado con restricciones de QoS desde la estructura de la composition, datos empiricos en tiempo de ejecución y (cuando estén disponibles) los resultados del análisis de complejidad. Este enfoque se puede aplicar a las orquestaciones de servicios con un control centralizado del flujo, así como a las coreografías con participantes multiples, siguiendo unas interacciones complejas que modifican su estado. El análisis del compartición de datos puede servir de apoyo para acciones de adaptación, como la paralelización, fragmentación y selección de los componentes, las cuales son basadas en dependencias funcionales y en el contenido de información en los mensajes, datos internos y las actividades de la composición, cuando se usan construcciones de control complejas, como bucles, bifurcaciones y flujos anidados. Tanto las dependencias funcionales como el contenido de información (descrito a través de algunos atributos definidos por el usuario) se pueden expresar usando una representación basada en la lógica de primer orden (claúsulas de Horn), y los resultados del análisis se pueden interpretar como modelos conceptuales basados en retículos. ABSTRACT Service-Oriented Computing (SOC) is a widely accepted paradigm for development of flexible, distributed and adaptable software systems, in which service compositions perform more complex, higher-level, often cross-organizational tasks using atomic services or other service compositions. In such systems, Quality of Service (QoS) properties, such as the performance, cost, availability or security, are critical for the usability of services and their compositions in concrete applications. Analysis of these properties can become more precise and richer in information, if it employs program analysis techniques, such as the complexity and sharing analyses, which are able to simultaneously take into account both the control and the data structures, dependencies, and operations in a composition. Computation cost analysis for service composition can support predictive monitoring and proactive adaptation by automatically inferring computation cost using the upper and lower bound functions of value or size of input messages. These cost functions can be used for adaptation by selecting service candidates that minimize total cost of the composition, based on the actual data that is passed to them. The cost functions can also be combined with the empirically collected infrastructural parameters to produce QoS bounds functions of input data that can be used to predict potential or imminent Service Level Agreement (SLA) violations at the moment of invocation. In mission-critical applications, an effective and accurate continuous QoS prediction, based on continuations, can be achieved by constraint modeling of composition QoS based on its structure, known data at runtime, and (when available) the results of complexity analysis. This approach can be applied to service orchestrations with centralized flow control, and choreographies with multiple participants with complex stateful interactions. Sharing analysis can support adaptation actions, such as parallelization, fragmentation, and component selection, which are based on functional dependencies and information content of the composition messages, internal data, and activities, in presence of complex control constructs, such as loops, branches, and sub-workflows. Both the functional dependencies and the information content (described using user-defined attributes) can be expressed using a first-order logic (Horn clause) representation, and the analysis results can be interpreted as a lattice-based conceptual models.

Diseño e implementación de un framework de funcionalidades Javascript en entornos de programación web

El presente documento aborda la problemática surgida en torno al desarrollo de una plataforma para gestionar las guías docentes de la Universidad Politécnica de Madrid, centrándose en el uso de las tecnologías Javascript, así como de lo algoritmos, plugins y bibliotecas auxiliares creadas y utilizadas. Por último, se muestran los resultados obtenidos del análisis y puesta en práctica de lo expuesto en el documento, así como conclusiones y sugerencias de futuras líneas de trabajo para este mismo proyecto. ---ABSTRACT---This document explains the problems found when developing a web service whose purpose is the management of learning guides at \Universidad Politecnica de Madrid". This final thesis focus on the use of Javascript technologies and the plugins, algorithms and auxiliar libraries used and developed. Finally, results of the analysis, development of the ideas exposed in this document, and conclusions and future working lines are presented.

A sharing-based approach to supporting adaptation in service compositions

Data-related properties of the activities involved in a service composition can be used to facilitate several design-time and run-time adaptation tasks, such as service evolution, distributed enactment, and instance-level adaptation. A number of these properties can be expressed using a notion of sharing. We present an approach for automated inference of data properties based on sharing analysis, which is able to handle service compositions with complex control structures, involving loops and sub-workflows. The properties inferred can include data dependencies, information content, domain-defined attributes, privacy or confidentiality levels, among others. The analysis produces characterizations of the data and the activities in the composition in terms of minimal and maximal sharing, which can then be used to verify compliance of potential adaptation actions, or as supporting information in their generation. This sharing analysis approach can be used both at design time and at run time. In the latter case, the results of analysis can be refined using the composition traces (execution logs) at the point of execution, in order to support run-time adaptation.

Sistemas web con alta disponibilidad en cloud

Este trabajo contiene el estudio de las tecnologías que se están usando actualmente en web, tratando de explicar cuáles son sus principales componentes, su objetivo y funcionamiento. En base a un supuesto teórico de un montaje para un servicio web con un número muy alto de usuarios, y basándose en las tecnologías estudiadas, se propone un posible montaje completo de un sistema, que sería capaz de gestionar correctamente todas las peticiones, evitando fallos y tiempos de indisponibilidad. Se a~nade un análisis teórico de los costes deribados de la implantación del sistema, comparándolo con un sistema web convencional, y otro análisis con el funcionamiento de una caché y los benéficos, en carga, derivados de su uso.---ABSTRACT---This work contains a study about new web technologies. Its objective is to explain the web technologies componentes with their particular usage and performance. Based on a theorical postulation about a preparation of a web service with a large number of users, and working with the studied technologies, a complete system assembling is proposed. This system will be able to attend all the incoming requests, without failures nor downtimes. It is attached a theorical study of the derivative costs associated to the system implementation, compared to a traditional one. In addition, another study is included with the work ow of a cache and the benefits derived of its usage in work terms.

A web-based application for the management and evaluation of tutoring requests in PBL-based massive laboratories

One important steps in a successful project-based-learning methodology (PBL) is the process of providing the students with a convenient feedback that allows them to keep on developing their projects or to improve them. However, this task is more difficult in massive courses, especially when the project deadline is close. Besides, the continuous evaluation methodology makes necessary to find ways to objectively and continuously measure students' performance without increasing excessively instructors' work load. In order to alleviate these problems, we have developed a web service that allows students to request personal tutoring assistance during the laboratory sessions by specifying the kind of problem they have and the person who could help them to solve it. This service provides tools for the staff to manage the laboratory, for performing continuous evaluation for all students and for the student collaborators, and to prioritize tutoring according to the progress of the student's project. Additionally, the application provides objective metrics which can be used at the end of the subject during the evaluation process in order to support some students' final scores. Different usability statistics and the results of a subjective evaluation with more than 330 students confirm the success of the proposed application.

The state of semantic technology today - overview of the first SEALS evaluation campaigns

This paper describes the first five SEALS Evaluation Campaigns over the semantic technologies covered by the SEALS project (ontology engineering tools, ontology reasoning tools, ontology matching tools, semantic search tools, and semantic web service tools). It presents the evaluations and test data used in these campaigns and the tools that participated in them along with a comparative analysis of their results. It also presents some lessons learnt after the execution of the evaluation campaigns and draws some final conclusions.