BioSWR - Semantic Web services Registry for Bioinformatics

Article About the Authors Metrics Comments Related Content Abstract Introduction Functionality Implementation Discussion Acknowledgments Author Contributions References Reader Comments (0) Figures Abstract Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/​under the LGPL license.

Gestión de la actividad no presencial y autoevaluación de competencias = Management of Student Learning Outside the Classroom and the Self-evaluation of Competences

Psychological Assessment is a core subject of Psychology studies, and of the university degree Human development, at the University of Girona and according to the University regulations, had 12 credits. Until the 2005-06 academic years, the student work conducted outside the classroom consisted of undertaking a psychological assessment that was written and handed in at the end of the course. From this the student obtained a qualification and a review if they applied for it In accordance with the European Credits for Higher Education, this subject was reduced to 9 credits, which is the equivalent of a total of 255 hours of in-class work and outside the classroom. In the 2006-07 academic year we created a guide to manage the student’s experiences outside the classroom, with the objective of encouraging the application of problem solving/critical thinking (Bloom, 1975), in line with the recommendations of the Catalonia Agency for University System Quality (2005). The guide includes: learning objectives, evaluation criterions, a description of activities, work week timetable for the whole course, programmed tutorials to review all steps of the psychological assessment process, and the use of a web-based virtual forum for the transfer of knowledge, analysis and constructive critiques of the assessment done by themselves and their colleagues

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.

Cross-Cultural Communication in Oncology: Challenges and Training Interests.

PURPOSE/OBJECTIVES: To survey oncology nurses and oncologists about difficulties in taking care of culturally and linguistically diverse patients and about interests in cross-cultural training.
. DESIGN: Descriptive, cross-sectional.
. SETTING: Web-based survey.
. SAMPLE: 108 oncology nurses and 44 oncologists. 
. METHODS: 31-item questionnaire derived from preexisting surveys in the United States and Switzerland.
. MAIN RESEARCH VARIABLES: Self-rated difficulties in taking care of culturally and linguistically diverse patients and self-rated interests in cross-cultural training.
. FINDINGS: All respondents reported communication difficulties in encounters with culturally and linguistically diverse patients. Respondents considered the absence of written materials in other languages, absence of a shared common language with patients, and sensitive subjects (e.g., end of life, sexuality) to be particularly problematic. Respondents also expressed a high level of interest in all aspects of cross-cultural training (task-oriented skills, background knowledge, reflexivity, and attitudes). Nurses perceived several difficulties related to care of migrants as more problematic than physicians did and were more interested in all aspects of cross-cultural training. 
. CONCLUSIONS: The need for cross-cultural training is high among oncology clinicians, particularly among nurses.
. IMPLICATIONS FOR NURSING: The results reported in the current study may help nurses in decision-making positions and educators in introducing elements of cross-cultural education into oncology curricula for nurses. Cross-cultural training should be offered to oncology nurses.

L'informatique: un outil remarquable pour l'enseignement de la médecine interne générale [The informatics: a remarkable tool for teaching general internal medicine].

INTERMED training implies a three week course, integrated in the "primary care module" for medical students in the first master year at the school of medicine in Lausanne. INTERMED uses an innovative teaching method based on repetitive sequences of e-learning-based individual learning followed by collaborative learning activities in teams, named Team-based learning (TBL). The e-learning takes place in a web-based virtual learning environment using a series of interactive multimedia virtual patients. By using INTERMED students go through a complete medical encounter applying clinical reasoning and choosing the diagnostic and therapeutic approach. INTERMED offers an authentic experience in an engaging and safe environment where errors are allowed and without consequences.

An interactive web-GIS tool for risk analysis: a case study in the Fella River basin, Italy

This paper presents a prototype of an interactive web-GIS tool for risk analysis of natural hazards, in particular for floods and landslides, based on open-source geospatial software and technologies. The aim of the presented tool is to assist the experts (risk managers) in analysing the impacts and consequences of a certain hazard event in a considered region, providing an essential input to the decision-making process in the selection of risk management strategies by responsible authorities and decision makers. This tool is based on the Boundless (OpenGeo Suite) framework and its client-side environment for prototype development, and it is one of the main modules of a web-based collaborative decision support platform in risk management. Within this platform, the users can import necessary maps and information to analyse areas at risk. Based on provided information and parameters, loss scenarios (amount of damages and number of fatalities) of a hazard event are generated on the fly and visualized interactively within the web-GIS interface of the platform. The annualized risk is calculated based on the combination of resultant loss scenarios with different return periods of the hazard event. The application of this developed prototype is demonstrated using a regional data set from one of the case study sites, Fella River of northeastern Italy, of the Marie Curie ITN CHANGES project.

International comparison of the German evidence-based S3-guidelines on the diagnosis and multimodal treatment of early and locally advanced gastric cancer, including adenocarcinoma of the lower esophagus.

BACKGROUND: Clinical guidelines are essential in implementing and maintaining nationwide stage-specific diagnostic and therapeutic standards. In 2011, the first German expert consensus guideline defined the evidence for diagnosis and treatment of early and locally advanced esophagogastric cancers. Here, we compare this guideline with other national guidelines as well as current literature. METHODS: The German S3-guideline used an approved development process with de novo literature research, international guideline adaptation, or good clinical practice. Other recent evidence-based national guidelines and current references were compared with German recommendations. RESULTS: In the German S3 and other Western guidelines, adenocarcinomas of the esophagogastric junction (AEG) are classified according to formerly defined AEG I-III subgroups due to the high surgical impact. To stage local disease, computed tomography of the chest and abdomen and endosonography are reinforced. In contrast, laparoscopy is optional for staging. Mucosal cancers (T1a) should be endoscopically resected "en-bloc" to allow complete histological evaluation of lateral and basal margins. For locally advanced cancers of the stomach or esophagogastric junction (≥T3N+), preferred treatment is preoperative and postoperative chemotherapy. Preoperative radiochemotherapy is an evidence-based alternative for large AEG type I-II tumors (≥T3N+). Additionally, some experts recommend treating T2 tumors with a similar approach, mainly because pretherapeutic staging is often considered to be unreliable. CONCLUSIONS: The German S3 guideline represents an up-to-date European position with regard to diagnosis, staging, and treatment recommendations for patients with locally advanced esophagogastric cancer. Effects of perioperative chemotherapy versus chemoradiotherapy are still to be investigated for adenocarcinoma of the cardia and the lower esophagus.

Análisis del entorno colaborativo creado para una experiencia de mobile learning

Se presentan los resultados de una investigación sobre las concepciones y usos de dispositivos móviles de un grupo de estudiantes que trabajaron en un entorno de aprendizaje colaborativo como parte un proceso de e-learning. Se emplearon dos métodos de investigación, en primer lugar el análisis del contenido de los mensajes de un foro de discusión enviados durante todo el curso, para recoger datos acerca del uso y la valoración que hacían del proceso de mobile learning. Posteriormente, mediante las entrevistas en profundidad, se analizó la percepción de mobile learning y los cambios producido durante el curso en el entorno colaborativo de aprendizaje. Los resultados indican que el entorno de intercambio creado amplifica la participación y colaboración entre los alumnos en el proceso de mobile learning, favoreciendo un mayor protagonismo de los estudiantes en una experiencia de aprendizaje online.

Student Journalism 2.0 : Testing Models for Participatory Learning in the Digital Age

Many educators and educational institutions have yet to integrate web-based practices into their classrooms and curricula. As a result, it can be difficult to prototype and evaluate approaches to transforming classrooms from static endpoints to dynamic, content-creating nodes in the online information ecosystem. But many scholastic journalism programs have already embraced the capabilities of the Internet for virtual collaboration, dissemination, and reader participation. Because of this, scholastic journalism can act as a test-bed for integrating web-based sharing and collaboration practices into classrooms. Student Journalism 2.0 was a research project to integrate open copyright licenses into two scholastic journalism programs, to document outcomes, and to identify recommendations and remaining challenges for similar integrations. Video and audio recordings of two participating high school journalism programs informed the research. In describing the steps of our integration process, we note some important legal, technical, and social challenges. Legal worries such as uncertainty over copyright ownership could lead districts and administrators to disallow open licensing of student work. Publication platforms among journalism classrooms are far from standardized, making any integration of new technologies and practices difficult to achieve at scale. And teachers and students face challenges re-conceptualizing the role their class work can play online.

Broadening the CRM domain of application to higher educational (e-learning) environments

In this paper, we reflect about the broadening of the field of application of CRM from the business domain to a wider context of relationships in which the inclusion of non-profit making organizations seems natural. In particular, we focus on analyzing the suitability of adopting CRM processes by universities and higher educational institutions dedicated to e-learning. This is an issue that, in our opinion, has much potential but has received little attention in research so far.

University teacher competences in a virtual teaching/learning environment : analysis of a teacher training experience

This paper attempts to shed light on the competencies a teacher must have inorder to teach in online university environments. We will relate a teacher trainingexperience, which was designed taking into account the methodological criteriaestablished in line with previous theoretical principles. The main objective of ouranalysis is to identify the achievements and difficulties of a specific formativeexperience, with the ultimate goal of assessing the suitability of this conceptualmethodologicalframework for the design of formative proposals aiming to contribute tothe development of teacher competencies for virtual environments.

Contenidos educativos en abierto

Peer-reviewed

Creating a research network for a successful e-portfolio design and implementation

The presence of e-portfolios in educational centres, companies and administrations has emergedstrongly during the last years by creating very different practices coming from different objectives and purposes. This situation has led researchers and practitioners to design and implement e-portfolios with little reference to previous knowledge of them; consequently, developments are disparate with many of the processes and dimensions used both in development and use being unnecessary complex. In order to minimize the inconveniences, unify these developmental processes and improve the resultsof implementation and use of e-portfolios, it seemed necessary to create a network of researchers, teachers and trainers coming from different universities and institutions of different kinds who are interested in the investigation and the practice of e-portfolios in Spain. Therefore, The Network on e-portfoliowas created in 2006, funded by the Spanish Ministry of Education and led by the UniversitatOberta de Catalunya. Besides the goals associatedwith the creation of this network and which wewanted to share with other European researchers and experts of other continents, we will also present in this paper some data concerned with the first study carried out on the use of e-portfolios in our country that shows where we are and which trends are the most important for the near future.

Learning 2.0 : concepts and experiences

E-learning arises in all educative contexts and levels with the use of information and communication technologies and massive access to internet connected computers. On the other hand, the fast development of social networking tools and web 2.0 technologies are producing an evolution of e-learning towards what is called a learning 2.0 paradigm. In this short paper weshall present the main technologies and pedagogical issues related to that new way of learning and how we can use them to improve the acquisition of competences and new knowledge.

Interactive Calculus in a Virtual Learning Environment

The teaching of higher level mathematics for technical students in a virtual learningenvironment poses some difficulties, but also opportunities, now specific to that virtuality.On the other hand, resources and ways to do now manly available in VLEs might soon extend to all kinds of environments.In this short presentation we will discuss anexperience carried at Universitat Oberta deCatalunya (UOC) involving (an on line university), first, the translation of LaTeX written existent materials to a web based format(specifically, a combination of XHTML andMathML), and then the integration of a symbolic calculator software (WIRIS) running as a Java applet embedded in the materials, intending to achieve an evolution from memorising concepts and repetitive algorithms to understanding and experiment concepts and the use of those algorithms.