Virtual Research Community Research Articles

A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations.

Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However, performing a successful simulation requires sufficient computational resources, familiarity with the simulation software, and experience in the setup of a system and the analysis of the resulting trajectories. These considerations become especially critical in large-scale parametric MD simulations. Offering such tools to a wide user community requires a robust and versatile, but user-friendly, facility for molecular dynamics simulations with access to vast computational resources. Here, we present the GROMACS grid-enabled Web portal for the setup and execution of molecular dynamics simulation on the WeNMR grid infrastructure, a distributed network of computational resources within the European Grid Initiative. The Web portal aims at ease-of-use through automated setup of the simulation system using best-practice protocols, yet allowing for tuning of key parameters. Alternatively, the simulation can be started from preconfigured GROMACS simulation systems. Performing multiple lengthy calculations using multiple processors on the WeNMR grid infrastructure ensures scalability. The combination of analysis routines for quality assurance and automatic recovery in case of failures provides a reliable platform for MD simulations. The GROMACS Web portal is embedded within the services of the WeNMR Virtual Research Community (VRC) accessible from http://www.wenmr.eu/wenmr/nmr-services . It is freely accessible upon registration with a valid X509 personal certificate with the enmr.eu Virtual Organization (VO).

Collaborative electronic infrastructures to accelerate taxonomic research

The discipline of taxonomy lives in a state of perpetual beta, constantly evolving as species hypotheses change to reflect the latest character evidence. Likewise, the electronic infrastructures that underpin taxonomic research are evolving to reflect the latest technical advances. This collection of articles illustrates how advances to research infrastructures are reciprocally changing the practice of taxonomy. The infrastructures have, in part, been developed through the EU funded ViBRANT project. This is the latest in a series of EU funded initiatives that aim to move taxonomy towards a more collaborative, electronic framework in an effort to accelerate the pace of biodiversity research. Through a platform of web-based informatics tools and services, ViBRANT project partners are building a framework that allows distributed groups of scientists to create their own virtual research communities that support biodiversity science. To mark the first year of the ViBRANT project we have brought together a set of reviews, essays and research articles that reflect some of the project highlights and illustrate a number of associated activities. Fittingly, many of the contributions are from researchers who have no direct support from the ViBRANT project, but have used or reviewed some aspect of the infrastructure. This marks an important transition from many EU funded infrastructure projects have typically focused on technical developments, and less on the communities that use these systems. A detailed review of data issues in the life sciences (Thessen and Patterson 2011) sets the tone for subsequent articles in this special issue, whose contributions broadly fall into three categories. The initial articles consider some of the major infrastructure platforms that support the production and management of biodiversity data. These include the EDIT Platform for Cybertaxonomy, Wiki-based approaches including BioWikiFarm and the Scratchpads Virtual Research Environment. Later articles provide deeper coverage of specialist areas of interest to taxonomic and biodiversity researchers. The topics covered include the mark-up (Penev et al. 2011) and management (King et al. 2011) of taxonomic literature, geospatial assessment of species distributions (Bachman et al. 2011) and licensing issues specific to life science data (Hagedorn et al. 2011). Finally, the special issue closes with a series of research and review papers that provide detailed use cases illustrating how these research infrastructures are being put into practice. These articles make up the majority of this special issue and are subdivided into the sociological analysis of how people are using these infrastructures, as well as the practical experience of biodiversity researchers developing taxonomic data with these systems. Highlights from this section include citizen science approaches to collecting species information by the COMBER Marine observation network (Arvanitidis et al. 2011) and the Australian Bush Blitz programme (Lambkin and Bartlett 2011); use of new tools for data publishing like the Global Biodiversity Information Facility (GBIF) Integrated Publishing Toolkit (IPT) and the DRYAD Data Repository; new forms of publication via “data papers” that allow checklists and identification keys to be formally published as structured datasets (e.g., Narwade et al. 2011); and finally new taxonomic revisions and species descriptions constructed from within the collaborative systems like XPER2 and Scratchpads. This diverse collection of articles illustrates how the paradigm of scholarly communication in taxonomy is being changed by new electronic infrastructures. These support new ways to collaborate and disseminate taxonomic information, facilitating greater reuse of the underlying data. The infrastructures described here are in many cases experimental, but illustrate a number of possible trajectories for how taxonomic data might be assembled and disseminated in the future. These infrastructures will continue to change and evolve, but it now seems certain that the future of taxonomy is increasingly digital, to the point that non-digital work is becoming invisible and perhaps irreverent to the next generation of scholars.

Personalized Knowledge Mining in Large Text Sets

The paper starts with a discussion of the concept of knowledge engineering, in particular ontological engineering. Consequently, the paper presents assumptions accepted as a basis for a group research on a radically personalized system of ontological knowledge mining, relying on the perspective of human centered computing and combining ontological concepts of the user with an ontology resulting from an automatic classification of a given set of textual data. The paper presents a pilot system PrOnto that supports research work in two aspects: searching for information interesting for a user according to her/his personalized ontological profile, and supporting research cooperation in a group of users (Virtual Research Community) according, e.g., to a comparison of such personalized ontological profiles. The paper concludes with suggestions concerning diverse applications of ontological engineering tools and future work.

E-Infrastructures for e-Science: A Global View

In the last 10 years, a new way of doing science is spreading in the world thank to the development of virtual research communities across many geographic and administrative boundaries. A virtual research community is a widely dispersed group of researchers and associated scientific instruments working together in a common virtual environment. This new kind of scientific environment, usually addressed as a “collaboratory”, is based on the availability of high-speed networks and broadband access, advanced virtual tools and Grid-middleware technologies which, altogether, are the elements of the e-Infrastructures. The European Commission has heavily invested in promoting this new way of collaboration among scientists funding several international projects with the aim of creating e-Infrastructures to enable the European Research Area and connect the European researchers with their colleagues based in Africa, Asia and Latin America. In this paper we describe the actual status of these e-Infrastructures and present a complete picture of the virtual research communities currently using them. Information on the scientific domains and on the applications supported are provided together with their geographic distribution.

Pilot Study of Aurora, a Social, Mobile-Phone-Based Emotion Sharing and Recording System

Emotion is a ubiquitous aspect of humanity that governs behavior in a number of ways and is linked inextricably with health. Pausing to evaluate one's emotional state in the face of decisions and reflecting on past patterns of emotion have been shown to improve behaviors. Further, social expression of emotion has been shown to directly improve health outcomes. While the virtual reality research community does not ignore emotion on the whole, there does exist a need to explore what roles emotional awareness and emotion sharing can play in this domain. A mobile-phone-based social emotion recording and sharing system, Aurora, was developed to provide individuals with a means to pause and evaluate their emotional state, reflect on past emotions, share emotions with others, and participate in socially supportive activities with peers. A study was conducted with 65 subjects to evaluate Aurora as a tool to encourage emotional reflection and awareness as well as social sharing of emotion. Users of Aurora reported an increased comfort in socially expressing emotion and were encouraged to share emotions, even with strangers. Subjects also reported liking reflecting on their emotional state and found it valuable. Subjects' behavior also suggested that the system encouraged individuals to reach out to one another in acts of social support. The Aurora system offers a tool for encouraging emotional awareness, emotion sharing, and socially supportive behavior. Such a tool could be impactful in numerous health settings where emotion is considered to be an important indicator of or influence on outcome, such as for weight loss, alcohol cessation, or cancer sufferers.

Building virtual collaborative research community using knowledge management approach

Many online communities nowadays are emphasized more on peer interactions and information sharing among members; very few online communities are built with knowledge management in nature supported by knowledge management system (KMS). This study aims to present a community of practice on how to effectively adopt a knowledge management system (KMS) to neutralize a cyber collaborative learning community for a research lab in a higher education setting. A longitudinal case for 7 years was used to analyze the retention and extension of participants’ community of practice experiences. Interviews were conducted for the comparison between experiences and theories. It was found that the transformations of tacit and explicit knowledge are in accordance with the framework of Nonaka’s model of knowledge management from which we elicit the strategies and suggestions to the adoption and implementation of virtual collaborative research community supported by KMS.

Exploring informed virtual sites through Michel Foucault's heterotopias

This papers starts with some mysterious contribution by Michel Foucault (1967) about heterotopias as special epistemological sites. With a recent case-study – an immersive virtual reality art project dealing with some ancient abbey reconstruction and managed by a French engineering school – we analyse the successive attempts to satisfy the system users by extending Foucault's heterotopology, which appears to be useful and creative for the Virtual Reality research communities.

Why Do Virtual Communities Regulate Speech?

Virtual community research argues that regulations restricting the kinds of speech in a virtual community decrease the utility to members. However, many virtual communities enact regulations on speech within the virtual community. This research explores the contradiction through a cross-case analysis of virtual communities. It explains the contradiction between research and practice using the theory of collective identity. Communication is important for creating collective identity in virtual communities. However, multiple collective identities can arise. When one collective identity within a virtual community defines itself as adversarial to another, silencing speech emerges as adversarial collective identity creates enduring noise and flames. When the target collective identity creates formal regulations suppressing the adversarial collective identity, communication to foster the target collective identity emerges.

Creating a Virtual Research Community: The University of Arizona PhD Program

To address the critical shortage of doctorally prepared nursing faculty and nurse scientists, The University of Arizona College of Nursing designed and implemented, as a virtual research community, an online doctor of philosophy (PhD) program. We are now completing our third year of the Online PhD Program and will admit our fourth cohort of students in August. In this article, we reflect on our progress to date and discuss what we have learned with nursing colleagues who may be considering this kind of change in their own programs. After describing the context for change, we discuss how the change was managed, including the planning and implementation of the program. We conclude with an evaluation of the process and early outcomes of the Online PhD Program from the authors' unique vantage points as program director, associate dean for academic affairs, and dean.

The Virtual Research Community: A New Arena of Scientific Communication

Over the last 30 years, the introduction of new communications techniques and information has generated a historical rupture, a paradigm break, resulting from innovative technological transformations. In this context, the virtual research community appears as a new cognitive social grouping for collective, interactive and interdisciplinary scientific practices, establishing selective patterns of relationships in the academy. Those new patterns are substituting the contact territory boundary, giving larger reach and speed to research, starting with their authors' interaction, independent of time and space. It is in this virtual arena that researchers feel changes in experiences, sharing of information, and mutual collaboration in research. The present study approaches the transformations of the scientific communication and points out the virtual communities' role in the current social context.

Comunidade virtual de pesquisa: nova arena da comunicação científica

Over the last 30 years, the introduction of new communications techniques and information has generated a historical rupture, a paradigm break, resulting from innovative technological transformations. In this context, the virtual research community appears as a new cognitive social grouping for collective, interactive and interdisciplinary scientific practices, establishing selective patterns of relationships in the academy. Those new patterns are substituting the contact territory boundary, giving larger reach and speed to research, starting with their authors’ interaction, independent of time and space. It is in this virtual arena that researchers feel changes in experiences, sharing of information, and mutual collaboration in research. The present study approaches the transformations of the scientific communication and points out the virtual communities’ role in the current social context.

Comunidade virtual de pesquisa: nova arena da comunicação científica

Over the last 30 years, the introduction of new communications techniques and information has generated a historical rupture, a paradigm break, resulting from innovative technological transformations. In this context, the virtual research community appears as a new cognitive social grouping for collective, interactive and interdisciplinary scientific practices, establishing selective patterns of relationships in the academy. Those new patterns are substituting the contact territory boundary, giving larger reach and speed to research, starting with their authors' interaction, independent of time and space. It is in this virtual arena that researchers feel changes in experiences, sharing of information, and mutual collaboration in research. The present study approaches the transformations of the scientific communication and points out the virtual communities' role in the current social context.

Mobile virtual communities research: a synthesis of current trends and a look at future perspectives

This article is a synthesis of current research trends in mobile virtual communities. It classifies Mobile Virtual Communities (MVCs) research into appropriate domains, and categorises the differen...

PKR: A Personalized Knowledge Recommendation System for Virtual Research Communities

This paper proposes a personalized explicit- and tacit-knowledge recommendation model for a virtual research community. The proposed model aims to recommend both useful journal documents (explicit knowledge) and community members who can discuss the information (tacit knowledge) on-line in real time. A middleware system, the personalized knowledge recommender (PKR) system, that was constructed from this model is presented. The model combines content-based (CB) and collaborative filtering (CF) methods, to make explicit and tacit knowledge recommendations. Unlike other similar systems, this system adapts CB and CF in different ways to provide users with not only “interest-related” documents for reference but also connections to the “related knowledge owners” for further on-line discussion. An e-journal paper recommendation for a virtual research community is used as an example to evaluate the performance of PKR in terms of mean absolute error, precision, recall and F-measure. PKR creates the specialty of explicit- and tacit-knowledge recommendations.

Mobile virtual communities research: a synthesis of current trends and a look at future perspectives

This article is a synthesis of current research trends in mobile virtual communities. It classifies Mobile Virtual Communities (MVCs) research into appropriate domains, and categorises the different types of virtual communities with respect to three criteria: the degree of virtualisation, the degree of mobility and the degree of cooperation. It also draws some conclusions on future research directions.

Enhancing business networks using social network based virtual communities

PurposeTo enhance an entrepreneur's business network through the integration of the social network concepts and design principles of virtual communities.Design/methodology/approachThis study documents the design and initial deployment of a virtual community case, Innovation Information Infrastructure, based on social network concepts.FindingsBasic design principles, deployment strategy, and future directions for social network‐based virtual communities are presented.Research limitations/implicationsBecause of resource and time constraints, only basic content service, communication tools, and transaction functions were implemented in the initial deployment. Future extensions of this study may include development of a personalized and intelligent information retrieval system utilizing data mining techniques, development of advanced communication features to promote active participation, and creation of automatic social network‐tracking tools to monitor an individual's network evolution.Practical implicationsSample designs are provided for researchers who are interested in conducting a similar study.Originality/valueThis study serves as a starting‐point for how theories from social network and virtual community research streams can be applied in creating a virtual community that facilitates transformation of knowledge into products and services, which in turn lead to greater economic prosperity.

Sustainable virtual communities: suggestions from the colonial model

While virtual community research has contributed to the understanding of the virtual community sustainability, a need for a systematic model exists. In this paper, we propose a model of sustainable virtual communities based on the sustainability properties of animal colonies in nature. The premise of our model is that if we manage to replicate the sustainability properties of colonial systems in virtual communities, they can become longer lasting. We also present the results of an exploratory case study. The study shows that colonial properties form a construct that predicts member perceptions of their community being sustainable. While our primary objective is the conceptual introduction of the colonial principles of sustainability, the case study provides some early indications that these principles may help design systems that can bind virtual communities more permanently.

Building a virtual research and teaching community

The Sloan Work and Family Research Network was created to provide web-based resources to individuals interested in work–family studies. The Network's website includes a database that contains over 5,000 citations/annotations of work–family research, a range of teaching resources for faculty and a newsletter. Experiences with the implementation of this project offer opportunities to consider the importance of devising community-building strategies for virtual networks that function as part of the ‘invisible college’.

Knowledge sharing in virtual communities: an e-business perspective

Thanks to availability of the Internet, virtual communities are proliferating at an unprecedented rate. In-depth understanding of virtual community dynamics can help us to address critical organizational and information systems issues such as communities-of-practice, virtual collaboration, and knowledge management. In this article, we develop a virtual community activity framework, integrating community knowledge sharing activity into business activities in the form of an e-business model. We examine how the level of community knowledge sharing activity leads to virtual community outcomes and whether such community outcomes are related to loyalty toward the virtual community service provider. Based on a field survey of 77 virtual communities currently operating in Freechal.com, one of Korea's largest Internet community service providers, we found that the level of community knowledge sharing activity is related to virtual community outcomes and such outcomes are significantly associated with loyalty to the virtual community service provider. These results imply that the level of community knowledge sharing activity may be a proper proxy for the state of health of a virtual community. Implications of the findings and future virtual community research directions are discussed.

Developing a virtual interdisciplinary research community in higher education

As multidisciplinary collaboration in both clinical and research settings is becoming a key aspect of contemporary health care, strategies to enhance interprofessional interaction in postgraduate research programmes can offer important experiences to facilitate on-going interprofessional relationships. This paper provides a retrospective appraisal of a strategy which used computermediated communication to develop a virtual community network, known as health_voice, accessed through a web page. The rationale for developing the network is presented, and the process of designing and establishing the web-site through an action research approach is described. The outcome of the strategy is reviewed with regard to the relationships between the real and virtual community. Reflections on the developmental process contextualise the initiative within a concept of a communityof-practice. It is acknowledged that the use of a virtual arena for communication within a research community involves a cultural change in the dynamics of higher degree teaching and learning. Future plans to further embed the virtual environment within a postgraduate research culture are given.