Computational framework to support integration of biomolecular and clinical data within a translational approach

Background The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. Results We have implemented an extension of Chado – the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Conclusions Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different “omics” technologies with patient’s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans webcite.

Progettazione e sviluppo di estensioni per AContent

In questo documento di tesi viene descritta la progettazione e la realizzazione di estensioni per il sistema di authoring AContent. L'idea è di creare un'estensione dell'authoring tool che implementi il concetto di template ovvero strumenti di grande efficacia e di facile utilizzo nelle fasi di redazione dei contenuti. Si prevede di aggiungerli ad AContent senza la necessità di integrare un intero motore di template ma utilizzando strutture dati esistenti e specifiche standard di e-learning. I servizi aggiuntivi da offrire agli autori sono stati organizzati secondo tre approcci diversi da cui sono emersi tre livelli di template. Il Template di Layout che determina l'aspetto grafico dei contenuti, il Template di Pagina che definisce la struttura di ogni singola pagina e il Template di Struttura che propone e imposta un modello per la struttura dell'intero contenuto didattico. Il documento è costituito da una seconda parte di progetto che va a coinvolgere il sistema ATutor e pone grande attenzione sulle caratteristiche di interoperabilità fra l'authoring AContent e il LCMS ATutor. Lo scopo è quello di estendere le funzionalità di integrazione dei contenuti del sistema così da presentare materiale didattico esterno archiviato in AContent. Viene trattata l'integrazione di LTI all'interno dei due sistemi considerati assegnando i ruoli di Tool Provider (AContent), fornitore di contenuti didattici remoti e Tool Consumer (ATutor), richiedente di tali contenuti. Sono considerati, infine, i due moduli di ATutor AContent Repository e External Tool che si occupano di importare materiale didattico da AContent tramite il Web Service REST. Si prevede la loro modifica affinché, attraverso il canale di comunicazione LTI stabilito, siano in grado di creare dei Live Content Link ovvero riferimenti a contenuti remoti (esterni alla piattaforma utilizzata) aggiornati in tempo reale. Infatti, a differenza di una normale importazione di un LO esterno è previsto che venga creano un "riferimento". In questo modo, la modifica di una pagina sul Tool Provider AContent si ripercuoterà istantaneamente su tutti i contenuti dei Tool Consumer che hanno instaurato un Live Content Link con il provider.

Integrated testing strategy (ITS) for bioaccumulation assessment under REACH

REACH (registration, evaluation, authorisation and restriction of chemicals) regulation requires that all the chemicals produced or imported in Europe above 1 tonne/year are registered. To register a chemical, physicochemical, toxicological and ecotoxicological information needs to be reported in a dossier. REACH promotes the use of alternative methods to replace, refine and reduce the use of animal (eco)toxicity testing. Within the EU OSIRIS project, integrated testing strategies (ITSs) have been developed for the rational use of non-animal testing approaches in chemical hazard assessment. Here we present an ITS for evaluating the bioaccumulation potential of organic chemicals. The scheme includes the use of all available data (also the non-optimal ones), waiving schemes, analysis of physicochemical properties related to the end point and alternative methods (both in silico and in vitro). In vivo methods are used only as last resort. Using the ITS, in vivo testing could be waived for about 67% of the examined compounds, but bioaccumulation potential could be estimated on the basis of non-animal methods. The presented ITS is freely available through a web tool.

Virtual Excursions: a new way to explore science in class

The educational platform Virtual Science Hub (ViSH) has been developed as part of the GLOBAL excursion European project. ViSH (http://vishub.org/) is a portal where teachers and scientist interact to create virtual excursions to science infrastructures. The main motivation behind the project was to connect teachers - and in consequence their students - to scientific institutions and their wide amount of infrastructures and resources they are working with. Thus the idea of a hub was born that would allow the two worlds of scientists and teachers to connect and to innovate science teaching. The core of the ViSH?s concept design is based on virtual excursions, which allow for a number of pedagogical models to be applied. According to our internal definition a virtual excursion is a tour through some digital context by teachers and pupils on a given topic that is attractive and has an educational purpose. Inquiry-based learning, project-based and problem-based learning are the most prominent approaches that a virtual excursion may serve. The domain specific resources and scientific infrastructures currently available on the ViSH are focusing on life sciences, nano-technology, biotechnology, grid and volunteer computing. The virtual excursion approach allows an easy combination of these resources into interdisciplinary teaching scenarios. In addition, social networking features support the users in collaborating and communicating in relation to these excursions and thus create a community of interest for innovative science teaching. The design and development phases were performed following a participatory design approach. An important aspect in this process was to create design partnerships amongst all actors involved, researchers, developers, infrastructure providers, teachers, social scientists, and pedagogical experts early in the project. A joint sense of ownership was created and important changes during the conceptual phase were implemented in the ViSH due to early user feedback. Technology-wise the ViSH is based on the latest web technologies in order to make it cross-platform compatible so that it works on several operative systems such as Windows, Mac or Linux and multi-device accessible, such as desktop, tablet and mobile devices. The platform has been developed in HTML5, the latest standard for web development, assuring that it can run on any modern browser. In addition to social networking features a core element on the ViSH is the virtual excursions editor. It is a web tool that allows teachers and scientists to create rich mash-ups of learning resources provided by the e-Infrastructures (i.e. remote laboratories and live webcams). These rich mash-ups can be presented in either slides or flashcards format. Taking advantage of the web architecture supported, additional powerful components have been integrated like a recommendation engine to provide personalized suggestions about educational content or interesting users and a videoconference tool to enhance real-time collaboration like MashMeTV (http://www.mashme.tv/).

Marco de diseño de la interacción para aplicaciones móviles

El desarrollo de aplicaciones móviles multiplataforma se ha convertido en una tarea compleja debido al alto crecimiento de dispositivos móviles y a la diversidad de plataformas que existen en el mercado. Tras identificar que las principales plataformas utilizadas por los usuarios a nivel mundial son iOS y Android y observar la evolución que han sufrido dichas plataformas desde un punto de vista de diseño de la interacción en los últimos años se establecen las bases para la realización del marco de diseño de la interacción en aplicaciones móviles. El marco de diseño pretende identificar la estructura de las aplicaciones en ambas plataformas y observar las similitudes y diferencias que existen entre las mismas. Por otra parte, se analizan, como parte del mismo, los elementos presentes en el diseño de la interacción de aplicaciones en las plataformas estudiadas con el fin de establecer similitudes y equivalencias entre los mismos. Para evaluar la viabilidad del marco propuesto, se ha llevado a cabo un caso de estudio en el que se aplica el marco sobre una aplicación real. Por último, se realiza una herramienta web con la que se permite a los usuarios poder acceder a la información propuesta en el marco de una forma más sencilla.---ABSTRACT---The mobile app development field has become a very complex task due to the increase of mobile devices and the diversity of the market existing platforms. After identifying that the most used platforms by the users are iOS and Android, and observing the evolution of both from the point of view of the interaction design, the basis for an interaction design frame are established. The design presents the basic structure of a mobile application in both platforms, identifying the existing similarities and differences among them. Moreover, the elements present in the design of the interaction are analysed, in order to establish similarities and equivalences among those elements. In addition, a case study was carried out in which the design frame was applied in a real application. Finally, a web tool which allow users to access the proposed information was developed, in order to have an easier access to the information.

Study on heuristic usability evaluation for mobile applications

Usability guidelines are a useful tool for the developers to improve interaction with systems. It includes knowledge of different disciplines related to usability and provides solutions and best practices to achieve the objectives of usability. Heuristic evaluation is one of the methods most widely used to evaluate and user interfaces. The objective of this study is to enrich the process of heuristic evaluation with the design guidelines focusing it on the evaluation of applications for mobile devices. As well as generate a homogeneous classification of guidelines content, in order to help that from design and development process, be included solutions and good practices provided by the guidelines. In order to achieve the objectives of this work, it is provides a method for generating heuristics for mobile applications, with which four applications were evaluated, and a web tool has also been developed that allows access to the content of the guidelines using the homogeneous classification of guidelines content. The results showed the ease and utility of performing heuristic evaluations using a set of heuristics focused on mobile applications.

Weblog sobre tecnología e Internet utilizando la metodología December

Este proyecto trata el desarrollo de un weblog sobre tecnología e internet siguiendo la Metodología de December, abordando todas sus etapas e incorporando otros aspectos a la metodología que han enriquecido el proyecto hasta su resultado final. Se pretende realizar una aplicación web con la funcionalidad de un weblog centrándose tanto en la parte del usuario final como del administrador de la web. Que este weblog sirva para compartir conocimientos de forma dinámica actualizándose con frecuencia y para usuarios con inquietudes tecnologías y con mayor o menor nivel de conocimientos. Se pone especial interés en la usabilidad de la herramienta y es tenida en cuenta a lo largo de todo el ciclo de vida de la metodología. Como punto de partida para estructurar la aplicación se toma como metodología de desarrollo la metodología December enfocada al desarrollo web y como a partir de ella se da forma a lo que hoy es el proyecto completo. Se tienen en cuenta cada una de sus etapas en las cuales se va avanzando para ir completando cada pieza del desarrollo final. Se intenta también en esta memoria abordar datos más técnicos de la herramienta, desde la elección de los lenguajes utilizados hasta el diseño de la estructura de base de datos, los procesos que intervienen en la aplicación y las decisiones más subjetivas de diseño de la interface web. En todo momento se ha intentado estructurar la memoria de tal forma que resultará clara y concisa, fácil de leer. Plasmando en ella todo el proceso de realización del proyecto. ABSTRACT This project involves the development of a technology and internet weblog following the December’s Methodology, covering all stages and adding other aspects to this methodology that have enriched the project to its final result. I plan to develop a web application with the functionality of a weblog focusing on both, the end user and the webmaster. A weblog to share knowledge in a dynamic and updated way, for users concerned with technologies and different levels of expertise. Special emphasis has been made on the usability of the web tool, taking this aspect into account through the entire methodology’s life cycle. To begin the development, the application structure is based on December’s methodology focused on web development. The whole project is built from this methodology. All the stages have been taken into account to complete each part of the final development. This project deals with technical data of the web tool, from the choice of the programming languages used to the design of the database structure, the processes involved in the application and the subjective decisions of interface design. At all times I have tried to structure the report in a clear, concise and easy to read way, reflecting it in the whole process of the project.

Measuring progress in eco-innovation. CEPS Working Document No. 409/June 2015

Eco-innovation has been identified as one of the key drivers of change that need to be harnessed for a sustainable future. Given the complexity of eco-innovation as a concept, there are various challenges to measuring its progress. This paper briefly explores the evolution of the concept of eco-innovation and emphasises its role in the EU 2020 strategy. It then provides an overview of the different measurement approaches and challenges associated with identifying and using indicators for measuring progress in eco-innovation. Within this context, the paper describes the added value and key features of the www.measuring-progress.eu web tool, which aims to improve the way in which policy-makers and others involved in the policy process can access, understand and use indicators for green economy and eco-innovation. The web tool was developed on the basis of a systematic overview by the NETGREEN research team of the large and fragmented body of work in the field of green economy indicators. The paper concludes with a number of messages for policy-makers in the field of the green economy.

Resource Efficiency Indicators for Policy-Making. CEPS Working Document No. 415/November 2015

In the EU, resource efficiency has been high on the political agenda since 2011, when the European Commission first included it as one of the seven flagship initiatives in its Europe 2020 Strategy for “smart, sustainable and inclusive growth”. Resource efficiency is not only considered an environmental necessity, but also a political, economic and security opportunity. This paper first stresses the benefits and opportunities for the EU of improving its resource efficiency. It then explains the added value of the www.measuring-progress.eu web tool, which aims to improve the way policy-makers and others involved in the policy process can access, understand and use indicators for resource efficiency. It provides practical examples of relevant indicators in the form of the EU Resource Efficiency Scoreboard and a case study showing how the web tool established by NETGREEN can be used in practice. The paper concludes with a number of policy messages.

Using linear algebra for protein structural comparison and classification.

In this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used efficiently to compare and classify protein structures into fold families. These signatures are built from the pattern of hydrophobic intrachain interactions using Singular Value Decomposition (SVD) and Latent Semantic Indexing (LSI) techniques. Considering proteins as documents and contacts as terms, we have built a retrieval system which is able to find conserved contacts in samples of myoglobin fold family and to retrieve these proteins among proteins of varied folds with precision of up to 80%. The classifier is a web tool available at our laboratory website. Users can search for similar chains from a specific PDB, view and compare their contact maps and browse their structures using a JMol plug-in.

Development and adoption of a web-based irrigation management tool for improved water use efficiency

Develop a web-based tool to assist farmers and consultants make strategic and tactical irrigation decisions.

Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains

Owing to high evolutionary divergence, it is not always possible to identify distantly related protein domains by sequence search techniques. Intermediate sequences possess sequence features of more than one protein and facilitate detection of remotely related proteins. We have demonstrated recently the employment of Cascade PSI-BLAST where we perform PSI-BLAST for many 'generations', initiating searches from new homologues as well. Such a rigorous propagation through generations of PSI-BLAST employs effectively the role of intermediates in detecting distant similarities between proteins. This approach has been tested on a large number of folds and its performance in detecting superfamily level relationships is similar to 35% better than simple PSI-BLAST searches. We present a web server for this search method that permits users to perform Cascade PSI-BLAST searches against the Pfam, SCOP and SwissProt databases. The URL for this server is http://crick.mbu.iisc.ernet.in/similar to CASCADE/CascadeBlast.html.

Invasionsoft: a web-enabled tool for invasive species colonization predictions

Predicting and averting the spread of invasive species is a core focus of resource managers in all ecosystems. Patterns of invasion are difficult to forecast, compounded by a lack of user-friendly species distribution model (SDM) tools to help managers focus control efforts. This paper presents a web-based cellular automata hybrid modeling tool developed to study the invasion pattern of lionfish (Pterois volitans/miles) in the western Atlantic and is a natural extension our previous lionfish study. Our goal is to make publically available this hybrid SDM tool and demonstrate both a test case (P. volitans/miles) and a use case (Caulerpa taxifolia). The software derived from the model, titled Invasionsoft, is unique in its ability to examine multiple default or user-defined parameters, their relation to invasion patterns, and is presented in a rich web browser-based GUI with integrated results viewer. The beta version is not species-specific and includes a default parameter set that is tailored to the marine habitat. Invasionsoft is provided as copyright protected freeware at http://www.invasionsoft.com.

ART: An ontology based tool for the translation of papers into Semantic Web format

To be presented at SIG/ISMB07 ontology workshop: http://bio-ontologies.org.uk/index.php To be published in BMC Bioinformatics. Sponsorship: JISC