The EU-ADR Web Platform: delivering advanced pharmacovigilance tools

PURPOSE: Pharmacovigilance methods have advanced greatly during the last decades, making post-market drug assessment an essential drug evaluation component. These methods mainly rely on the use of spontaneous reporting systems and health information databases to collect expertise from huge amounts of real-world reports. The EU-ADR Web Platform was built to further facilitate accessing, monitoring and exploring these data, enabling an in-depth analysis of adverse drug reactions risks.METHODS: The EU-ADR Web Platform exploits the wealth of data collected within a large-scale European initiative, the EU-ADR project. Millions of electronic health records, provided by national health agencies, are mined for specific drug events, which are correlated with literature, protein and pathway data, resulting in a rich drug-event dataset. Next, advanced distributed computing methods are tailored to coordinate the execution of data-mining and statistical analysis tasks. This permits obtaining a ranked drug-event list, removing spurious entries and highlighting relationships with high risk potential.RESULTS: The EU-ADR Web Platform is an open workspace for the integrated analysis of pharmacovigilance datasets. Using this software, researchers can access a variety of tools provided by distinct partners in a single centralized environment. Besides performing standalone drug-event assessments, they can also control the pipeline for an improved batch analysis of custom datasets. Drug-event pairs can be substantiated and statistically analysed within the platform's innovative working environment.CONCLUSIONS: A pioneering workspace that helps in explaining the biological path of adverse drug reactions was developed within the EU-ADR project consortium. This tool, targeted at the pharmacovigilance community, is available online at https://bioinformatics.ua.pt/euadr/. Copyright © 2012 John Wiley & Sons, Ltd.

Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree.

BACKGROUND: Available methods to simulate nucleotide or amino acid data typically use Markov models to simulate each position independently. These approaches are not appropriate to assess the performance of combinatorial and probabilistic methods that look for coevolving positions in nucleotide or amino acid sequences. RESULTS: We have developed a web-based platform that gives a user-friendly access to two phylogenetic-based methods implementing the Coev model: the evaluation of coevolving scores and the simulation of coevolving positions. We have also extended the capabilities of the Coev model to allow for the generalization of the alphabet used in the Markov model, which can now analyse both nucleotide and amino acid data sets. The simulation of coevolving positions is novel and builds upon the developments of the Coev model. It allows user to simulate pairs of dependent nucleotide or amino acid positions. CONCLUSIONS: The main focus of our paper is the new simulation method we present for coevolving positions. The implementation of this method is embedded within the web platform Coev-web that is freely accessible at http://coev.vital-it.ch/, and was tested in most modern web browsers.

Global research alliance modelling platform (GRAMP): an open web platform for modelling greenhouse gas emissions from agro-ecosystems

Carbon (C) and nitrogen (N) process-based models are important tools for estimating and reporting greenhouse gas emissions and changes in soil C stocks. There is a need for continuous evaluation, development and adaptation of these models to improve scientific understanding, national inventories and assessment of mitigation options across the world. To date, much of the information needed to describe different processes like transpiration, photosynthesis, plant growth and maintenance, above and below ground carbon dynamics, decomposition and nitrogen mineralization. In ecosystem models remains inaccessible to the wider community, being stored within model computer source code, or held internally by modelling teams. Here we describe the Global Research Alliance Modelling Platform (GRAMP), a web-based modelling platform to link researchers with appropriate datasets, models and training material. It will provide access to model source code and an interactive platform for researchers to form a consensus on existing methods, and to synthesize new ideas, which will help to advance progress in this area. The platform will eventually support a variety of models, but to trial the platform and test the architecture and functionality, it was piloted with variants of the DNDC model. The intention is to form a worldwide collaborative network (a virtual laboratory) via an interactive website with access to models and best practice guidelines; appropriate datasets for testing, calibrating and evaluating models; on-line tutorials and links to modelling and data provider research groups, and their associated publications. A graphical user interface has been designed to view the model development tree and access all of the above functions.

A flexible open source web platform to facilitate Learning Object evaluation

Systematic evaluation of Learning Objects is essential to make high quality Web-based education possible. For this reason, several educational repositories and e-Learning systems have developed their own evaluation models and tools. However, the differences of the context in which Learning Objects are produced and consumed suggest that no single evaluation model is sufficient for all scenarios. Besides, no much effort has been put in developing open tools to facilitate Learning Object evaluation and use the quality information for the benefit of end users. This paper presents LOEP, an open source web platform that aims to facilitate Learning Object evaluation in different scenarios and educational settings by supporting and integrating several evaluation models and quality metrics. The work exposed in this paper shows that LOEP is capable of providing Learning Object evaluation to e-Learning systems in an open, low cost, reliable and effective way. Possible scenarios where LOEP could be used to implement quality control policies and to enhance search engines are also described. Finally, we report the results of a survey conducted among reviewers that used LOEP, showing that they perceived LOEP as a powerful and easy to use tool for evaluating Learning Objects.

Visualization of flow fields in the web platform

Visualization of vector fields plays an important role in research activities nowadays -- Web applications allow a fast, multi-platform and multi-device access to data, which results in the need of optimized applications to be implemented in both high-performance and low-performance devices -- Point trajectory calculation procedures usually perform repeated calculations due to the fact that several points might lie over the same trajectory -- This paper presents a new methodology to calculate point trajectories over highly-dense and uniformly-distributed grid of points in which the trajectories are forced to lie over the points in the grid -- Its advantages rely on a highly parallel computing architecture implementation and in the reduction of the computational effort to calculate the stream paths since unnecessary calculations are avoided, reusing data through iterations -- As case study, the visualization of oceanic currents through in the web platform is presented and analyzed, using WebGL as the parallel computing architecture and the rendering Application Programming Interface

Prototype of a web-based participative decision support platform in natural hazards and risk management

This paper presents the current state and development of a prototype web-GIS (Geographic Information System) decision support platform intended for application in natural hazards and risk management, mainly for floods and landslides. This web platform uses open-source geospatial software and technologies, particularly the Boundless (formerly OpenGeo) framework and its client side software development kit (SDK). The main purpose of the platform is to assist the experts and stakeholders in the decision-making process for evaluation and selection of different risk management strategies through an interactive participation approach, integrating web-GIS interface with decision support tool based on a compromise programming approach. The access rights and functionality of the platform are varied depending on the roles and responsibilities of stakeholders in managing the risk. The application of the prototype platform is demonstrated based on an example case study site: Malborghetto Valbruna municipality of North-Eastern Italy where flash floods and landslides are frequent with major events having occurred in 2003. The preliminary feedback collected from the stakeholders in the region is discussed to understand the perspectives of stakeholders on the proposed prototype platform.

Implementação de plataforma web e android no âmbito da associação Anddvis

Trabalho de Projeto apresentado ao Instituto Superior de Contabilidade e Administração do Porto para a obtenção do grau de Mestre em Marketing Digital, sob orientação do Mestre Paulo Gonçalves

RealCrono –sistema de difusão de resultados em tempo real na web

A velocidade de difusão de conteúdos numa plataforma web, assume uma elevada relevância em serviços onde a informação se pretende atualizada e em tempo real. Este projeto de Mestrado, apresenta uma abordagem de um sistema distribuído de recolher e difundir resultados em tempo real entre várias plataformas, nomeadamente sistemas móveis. Neste contexto, tempo real entende-se como uma diferença de tempo nula entre a recolha e difusão, ignorando fatores que não podem ser controlados pelo sistema, como latência de comunicação e tempo de processamento. Este projeto tem como base uma arquitetura existente de processamento e publicação de resultados desportivos, que apresentava alguns problemas relacionados com escalabilidade, segurança, tempos de entrega de resultados longos e sem integração com outras plataformas. Ao longo deste trabalho procurou-se investigar fatores que condicionassem a escalabilidade de uma aplicação web dando ênfase à implementação de uma solução baseada em replicação e escalabilidade horizontal. Procurou-se também apresentar uma solução de interoperabilidade entre sistemas e plataformas heterogêneas, mantendo sempre elevados níveis de performance e promovendo a introdução de plataformas móveis no sistema. De várias abordagens existentes para comunicação em tempo real sobre uma plataforma web, adotou-se um implementação baseada em WebSocket que elimina o tempo desperdiçado entre a recolha de informação e sua difusão. Neste projeto é descrito o processo de implementação da API de recolha de dados (Collector), da biblioteca de comunicação com o Collector, da aplicação web (Publisher) e sua API, da biblioteca de comunicação com o Publisher e por fim a implementação da aplicação móvel multi-plataforma. Com os componentes criados, avaliaram-se os resultados obtidos com a nova arquitetura de forma a aferir a escalabilidade e performance da solução criada e sua adaptação ao sistema existente.

Post-MAPS: An interactive acquisition platform for gastroenterology

Post-MAPS is a web platform that collects gastroenterological exam data from several european hospital centers, to be used in future clinical studies and was developed in partnership with experts from the gastroenterological area and information technology (IT) technicians. However, although functional, this platform has some issues that are crucial for its functioning, and can render user interaction unpleasant and exhaustive. Accordingly, we proposed the development of a new web platform, in which we aimed for an improvement in terms of usability, data uni cation and interoperability. Therefore, it was necessary to identify and study different ways of acquiring clinical data and review some of the existing clinical databases in order to understand how they work and what type of data they store, as well as their impact and contribution to clinical knowledge. Closely linked to the data model is the ability to share data with other systems, so, we also studied the concept of interoperability and analyzed some of the most widely used international standards, such as DICOM, HL7 and openEHR. As one of the primary objectives of this project was to achieve a better level of usability, practices related to Human Computer-Interaction, such as requirement analysis, creation of conceptual models, prototyping, and evaluation were also studied. Before we began the development, we conducted an analysis of the previous platform, from a functional point of view, which allowed us to gather not only a list of architectural and interface issues, but also a list of improvement opportunities. It was also performed a small preliminary study in order to evaluate the platform's usability, where we were able to realize that perceived usability is different between users, and that, in some aspects, varies according to their location, age and years of experience. Based on the information gathered during the platform's analysis and in the conclusions of the preliminary study, a new platform was developed, prepared for all potential users, from the inexperienced to the most comfortable with technology. It presents major improvements in terms of usability, also providing several new features that simplify the users' work, improving their interaction with the system, making their experience more enjoyable.

Web-assisted tobacco intervention in Portuguese : intentions to make behavioural changes and behavioural changes

ABSTRACT - The problem of how to support “intentions to make behavioural changes” (IBC) and “behaviour changes” (BC) in smoking cessation when there is a scarcity of resources is a pressing issue in public health terms. The present research focuses on the use of information and communications technologies and their role in smoking cessation. It is developed in Portugal after the ratification of WHO Framework Convention on Tobacco Control (on 8 November 2005). The prevalence of smokers over fifteen years of age within the population stood at 20.9% (30.9% for men and 11.8% for women). While the strategy of helping people to quit smoking has been emphasised at National Health Service (NHS) level, the uptake of cessation assistance has exceeded the capacity of the service. This induced the search of new theoretical and practical venues to offer alternative options to people willing to stop smoking. Among these, the National Health Plan (NHP) of Portugal (2004-2010), identifies the use of information technologies in smoking cessation. eHealth and the importance of health literacy as a means of empowering people to make behavioural changes is recurrently considered an option worth investigating. The overall objective of this research is to understand, in the Portuguese context, the use of the Internet to help people to stop smoking. Research questions consider factors that may contribute to “intentions to make behavioural changes” (IBC) and “behavioural changes” (BC) while using a Web-Assisted Tobacco Intervention Probe (WATIP). Also consideration is given to the trade-off on the use of the Web as a tool for smoking cessation: can it reach a vast number of people for a small cost (efficiency) demonstrating to work in the domain of smoking cessation (efficacy)”? In addition to the introduction, there is a second chapter in which the use of tobacco is discussed as a public health menace. The health gains achieved by stopping smoking and the means of quitting are also examined, as is the use of the Internet in smoking cessation. Then, several research issues are introduced. These include background theory and the theoretical framework for the Sense of Coherence. The research model is also discussed. A presentation of the methods, materials and of the Web-Assisted Tobacco Intervention Probe (WATIP) follows. In chapter four the results of the use of the Web-Assisted Tobacco Intervention Probe (WATIP) are presented. This study is divided into two sections. The first describes results related to quality control in relation to the Web-Assisted Tobacco Intervention Probe (WATIP) and gives an overview of its users. Of these, 3,150 answered initial eligibility questions. In the end, 1,463 met all eligibility requirements, completed intake, decided on a day to quit smoking (Dday) and declared their “intentions to make behavioural changes” (IBC) while a second targeted group of 650 did not decide on a Dday. With two quit attempts made before joining the platform, most of the participants had experienced past failures while wanting to stop. The smoking rate averaged 21 cigarettes per day. With a mean age of 35, of the participants 55% were males. Among several other considerations, gender and the Sense of Coherence (SOC) influenced the success of participants in their IBC and endeavour to set quit dates. The results of comparing males and females showed that, for current smokers, establishing a Dday was related to gender differences, not favouring males (OR=0.76, p<0.005). Belonging to higher Socio-economic strata (SES) was associated with the intention to consider IBC (when compared to lower SES condition) (OR=1.57, p<0.001) and higher number of school years (OR=0.70, p<0.005) favoured the decision to smoking cessation. Those who demonstrated higher confidence in their likelihood of success in stopping in the shortest time had a higher rate of setting a Dday (OR=0.51, p<0.001). There were differences between groups in IBC reflecting the high and low levels of the SOC score (OR=1.43, p=0.006), as those who considered setting a Dday had higher levels of SOC. After adjusting for all variables, stages of readiness to change and SOC were kept in the model. This is the first Arm of this research where the focus is a discussion of the system’s implications for the participants’ “intentions to make behavioural changes” (IBC). Moreover, a second section of this study (second Arm) offers input collected from 77 in-depth interviews with the Web-Assisted Tobacco Intervention Probe (WATIP) users. Here, “Behaviour Change” (BC) and the usability of the platform are explored a year after IBC was declared. A percentage of 32.9% of self-reported, 12-month quitters in continuous abstinence from smoking from Dday to the 12-month follow- up point of the use of the Web-Assisted Tobacco Intervention Probe (WATIP) has been assessed. Comparing the Sense of Coherence (SOC) scores of participants by their respective means, according to the two groups, there was a significant difference in these scores of non smokers (BC) (M=144,66, SD=22,52) and Sense of Coherence (SOC) of smokers (noBC) (M=131,51, SD=21,43) p=0.014. This WATIP strategy and its contents benefit from the strengthening of the smoker’s sense of coherence (SOC), so that the person’s progress towards a life without tobacco may be experienced as comprehensible, manageable and meaningful. In this sample the sense of coherence (SOC) effect is moderate although it is associated with the day to quit smoking (Dday). Some of the limitations of this research have to do with self-selection bias, sample size (power) and self-reporting (no biochemical validation). The enrolment of participants was therefore not representative of the smoking population. It is not possible to verify the Web-Assisted Tobacco Intervention Probe (WATIP) evaluation of external validity; consequently, the results obtained cannot be applied generalized. No participation bias is provided. Another limitation of this study is the associated limitations of interviews. Interviewees’ perception that fabricating answers could benefit them more than telling the simple truth in response to questions is a risk that is not evaluated (with no external validation like measuring participants’ carbon monoxide levels). What emerges in this analysis is the relevance of the process that leads to the establishment of the quit day (Dday) to stop using tobacco. In addition, technological issues, when tailoring is the focus, are key elements for scrutiny. The high number of dropouts of users of the web platform mandates future research that should concentrate on the matters of the user-centred design of portals. The focus on gains in health through patient-centred care needs more research, so that technology usability be considered within the context of best practices in smoking cessation.

Implementación de aplicaciones y herramientas de post-procesamiento de imágenes médicas vía web

Con la creciente generación de resonancias magnéticas, los servicios de radiología necesitan aplicaciones que les faciliten el trabajo de acceso remoto a los datos y a las herramientas que utilicen para la extracción de datos para realizar sus diagnósticos. El objetivo de este proyecto es el de estudiar e integrar en la plataforma web del grupo de Imagen Médica del PIC llamada PICNIC (PIC NeuroImaging Center) un conjunto de aplicaciones para el estudio y procesamiento de neuroimagen con la implementación de herramientas software en la plataforma grid del PIC.

Plataforma para la búsqueda de talento usando programario libre y web 2.0

El objetivo de este proyecto es el de crear una plataforma para conectar a empresas con la necesidad de cubrir puestos de trabajo muy concretos con los mejores candidatos. Más allá del proyecto descrito en este documento, se pretende crear una empresa integradora de servicios de terceros tanto para empresas como para candidatos. Este proyecto se centra en el desarrollo de una plataforma Web basada en programario libre. La plataforma gira entorno a un portal que integra servicios de búsqueda de candidatos, reclutamiento y selección de personal. El portal utilizará la Web 2.0 y las redes sociales para llevar a cabo su cometido. El portal está disponible en http://www.sntalent.com.

WebGraphEd, an open source graph drawing editor for the web

WebGraphEd is an open source software for graph visualization and manipulation. It is especially designed to work for the web platform through a web browser. The web application has been written in JavaScript and compacted later, which makes it a very lightweight software. There is no need of additional software, and the only requirement is to have an HTML5 compliant browser. WebGraphEd works with scalable vector graphics (SVG), which it makes possible to create lossless graph drawings.

Integration of SCORM packages into web games

This paper presents a model that enables the integration of SCORM packages into web games. It is based on the fact that SCORM packages are prepared to be integrated into Learning Management Systems and to communicate with them. Hence in a similar way they can also be integrated into web games. The application of this model results in the linkage between the Learning Objects inside the package and specific actions or conditions in the game. The educational content will be shown to the players when they perform these actions or the conditions are met. For example, when they need a special weapon they will have to consume the Learning Object to get it. Based on this model we have developed an open source web platform which main aim is to facilitate teachers the creation of educational games. They can select existing SCORM packages or upload their own ones and then select a game template in which the Learning Objects will be integrated. The resulting educational game will be available online. Details about the model and the developed platform are explained in this paper. Also links to the platform and an example of a generated game will be provided.