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.

Digital libraries for the preservation of research methods and associated artifacts

New digital artifacts are emerging in data-intensive science. For example, scientific workflows are executable descriptions of scientific procedures that define the sequence of computational steps in an automated data analysis, supporting reproducible research and the sharing and replication of best-practice and know-how through reuse. Workflows are specified at design time and interpreted through their execution in a variety of situations, environments, and domains. Hence it is essential to preserve both their static and dynamic aspects, along with the research context in which they are used. To achieve this, we propose the use of multidimensional digital objects (Research Objects) that aggregate the resources used and/or produced in scientific investigations, including workflow models, provenance of their executions, and links to the relevant associated resources, along with the provision of technological support for their preservation and efficient retrieval and reuse. In this direction, we specified a software architecture for the design and implementation of a Research Object preservation system, and realized this architecture with a set of services and clients, drawing together practices in digital libraries, preservation systems, workflow management, social networking and Semantic Web technologies. In this paper, we describe the backbone system of this realization, a digital library system built on top of dLibra.

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.

Videoconference capacity Leasing on Hybrid Clouds.

This paper proposes a new methodology focused on implementing cost effective architectures on Cloud Computing systems. With this methodology the paper presents some disadvantages of systems that are based on single Cloud architectures and gives some advices for taking into account in the development of hybrid systems. The work also includes a validation of these ideas implemented in a complete videoconference service developed with our research group. This service allows a great number of users per conference, multiple simultaneous conferences, different client software (requiring transcodification of audio and video flows) and provides a service like automatic recording. Furthermore it offers different kinds of connectivity including SIP clients and a client based on Web 2.0. The ideas proposed in this article are intended to be a useful resource for any researcher or developer who wants to implement cost effective systems on several Clouds

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.

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.

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.

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.

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.

Standing together for reproducibility in large-scale computing: report on reproducibility@XSEDE

This is the final report on reproducibility@xsede, a one-day workshop held in conjunction with XSEDE14, the annual conference of the Extreme Science and Engineering Discovery Environment (XSEDE). The workshop's discussion-oriented agenda focused on reproducibility in large-scale computational research. Two important themes capture the spirit of the workshop submissions and discussions: (1) organizational stakeholders, especially supercomputer centers, are in a unique position to promote, enable, and support reproducible research; and (2) individual researchers should conduct each experiment as though someone will replicate that experiment. Participants documented numerous issues, questions, technologies, practices, and potentially promising initiatives emerging from the discussion, but also highlighted four areas of particular interest to XSEDE: (1) documentation and training that promotes reproducible research; (2) system-level tools that provide build- and run-time information at the level of the individual job; (3) the need to model best practices in research collaborations involving XSEDE staff; and (4) continued work on gateways and related technologies. In addition, an intriguing question emerged from the day's interactions: would there be value in establishing an annual award for excellence in reproducible research? Overview

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.

Service Capacity Reserve under Uncertainty by Hospital’s ER Analogies: A Practical Model for Car Services

We define a capacity reserve model to dimension passenger car service installations according to the demographic distribution of the area to be serviced by using hospital?s emergency room analogies. Usually, service facilities are designed applying empirical methods, but customers arrive under uncertain conditions not included in the original estimations, and there is a gap between customer?s real demand and the service?s capacity. Our research establishes a valid methodology and covers the absence of recent researches and the lack of statistical techniques implementation, integrating demand uncertainty in a unique model built in stages by implementing ARIMA forecasting, queuing theory, and Monte Carlo simulation to optimize the service capacity and occupancy, minimizing the implicit cost of the capacity that must be reserved to service unexpected customers. Our model has proved to be a useful tool for optimal decision making under uncertainty integrating the prediction of the cost implicit in the reserve capacity to serve unexpected demand and defining a set of new process indicators, such us capacity, occupancy, and cost of capacity reserve never studied before. The new indicators are intended to optimize the service operation. This set of new indicators could be implemented in the information systems used in the passenger car services.

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.

PubDNA Finder in a Nutshell. Searching the Life Sciences Literature with Sequences of Nucleic Acids

Biomedical researchers and clinicians working with molecular technologies in routine clinical practice often need to review the available literature to gather information regarding specific sequences of nucleic acids. This includes, for instance, finding articles related to a concrete DNA sequence, or identifying empirically-validated primer/probe sequences to evaluate the presence of different micro-organisms. Unfortunately, these hard and time-consuming tasks often need to be manually performed by researchers themselves since no publicly available biomedical literature search engine, e.g. PubMed, PubMed Central (PMC), etc., provides the required search functionalities. In this article, we describe PubDNA Finder, a web service that enables users to perform advanced searches on PubMed Central-indexed full text articles with sequences of nucleic acids