Interactive Web Pages Research Articles

Universal Activation Index for Class A GPCRs.

An index of the activation of Class A G-protein-coupled receptors (GPCRs) has been trained using interhelix distances from a series of microsecond molecular-dynamics simulations and tested for 268 published X-ray structures. In a three-class model that includes intermediate structures, 63% of the active structures are classified in agreement with the experimental assignment, 81% of the intermediate structures, and 89% of the inactives. An alternative two-state model classifies 94% of the actives and 99% of the inactives correctly. The intermediate structures are distributed 2:1 between actives and inactives. X-ray structures with protein nanobodies give good agreement between the assigned activation state and the predictions of the model, whereby many active nanobody structures are predicted to be weakly active. The five interhelix Cα-Cα distances that occur in the model relate clearly to the established activation mechanism. The model is available as a Python script or via an interactive web page. It can thus be used to classify both experimental and computational GPCR structures.

An introduction to classical molecular dynamics simulation for experimental scattering users.

Classical molecular dynamics simulations are a common component of multi-modal analyses of scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a 'black box' analysis technique. This article describes an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open-source software repository, which can be freely copied, modified and redistributed by educators. The topics covered in this OER include classical atomistic modelling, parameterizing interatomic potentials, molecular dynamics simulations, typical sources of error and some of the approaches to using simulations in the analysis of scattering data.

Internet-mediated automation of a cascade control system-an Engineering laboratory experiment

The paper aims to enhance the controllability of a standalone cascade control system with Internet architecture and promote the system to be accessible by remote students. The user interactive web page is developed by using platform independent ASP.NET language and enabled with both monitoring and controlling functionalities. The Internet transmission time delays that are associated with both feed-forward and feedback channels are compensated by using model predictive controller. The performance of cascade control system with and without compensation is validated by measuring indices, such as rise time, peak time and settling time, and also integral square error and integral absolute error. Access privileges among web page users have been added to ensure simultaneous operations as well as security. The cascade control system is an engineering laboratory experiment interfaced with a dedicated computer by using MODBUS protocol and it is made available to the remote students. The user perception analysis is carried out by using a set of questionnaire that observes 85% of positive feedback.

The ICES Working Group on Oceanic Hydrography: A Bridge From In-situ Sampling to the Remote Autonomous Observation Era

The ICES (International Council for the Exploration of the Sea) Working Group on Oceanic Hydrography (WGOH) was established in the late 1970’s with the aim of gathering experts in physical oceanography to provide regular science-based assessments of the North Atlantic hydrographical condition (basically termohaline fields). From the beginning, the WGOH has relied on repeated long-term in-situ sampling at key sites around the North Atlantic, the Nordic Seas and adjacent shelf seas. An annual Report on Ocean Climate (IROC), produced by the WGOH since the late 1990’s, summarizes trends in regional hydrography and identifies patterns linking these changes across the North Atlantic. Regional analyses are prepared by local experts who are directly involved in the monitoring programs responsible for collecting data presented in the report. An interactive webpage created in 2013 allows users to browse and download data that inform the IROC. Within the last two decades the physical oceanography community has evolved quickly incor- porating technological advances such as autonomous devices into classical in-situ sampling programs. The WGOH has embraced such technological developments without diverting focus from ongoing in-situ long-term monitoring programs. Having longstanding experience synthe- sizing data and expertise from a large number of operational programs spanning an extensive international footprint, the WGOH has a unique perspective to offer the global ocean observing community. Here we discuss how we might foster connections with ICES to benefit the GOOS (Global Ocean Observing System) community.

Keanu: a novel visualization tool to explore biodiversity in metagenomes

BackgroundOne of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing FASTQ sequencing data, visualizing which organisms are present in the data can be useful, especially with metagenomics data or data suspected to be contaminated. Here, we describe the development and application of a command-line tool, Keanu, for visualizing and exploring sample content in metagenomics data. We developed Keanu as an interactive tool to make viewing complex data easier.ResultsKeanu, a tool for exploring sequence content, helps a user to understand the presence and abundance of organisms in a sample by analyzing alignments against a database that contains taxonomy data and displaying them in an interactive web page. The content of a sample can be presented either as a collapsible tree, with node size indicating abundance, or as a bilevel partition graph, with arc size indicating abundance. Here, we illustrate how Keanu works by exploring shotgun metagenomics data from a sample collected from a bluff that contained paleosols and a krotovina in an alpine site in Ft. Greely, Alaska.ConclusionsKeanu provides a simple means by which researchers can explore and visualize species present in sequence data generated from complex communities and environments. Keanu is written in Python and is freely available at https://github.com/IGBB/keanu.

The art of the digital proposal: Bring your fundraising cases to life

Today’s donors are savvy, innovative and dynamic — and the fundraising proposals gift officers submit to them should be the same. Readers will learn how to go beyond the standard Word document by creating digital fundraising proposals that are as exciting and creative as their students, faculty and institution. Interactive maps, clickable charts and animated and photographic elements will bring proposals to life, truly impress donors and potentially increase fundraising. In this paper, fundraising professionals will get tips to consider which donors will gravitate to which proposal formats — Word documents, designed pieces and PowerPoint presentations (PPTs) or interactive webpages. They will learn the interactive and visual elements that make a digital proposal compelling and explore some tips and tricks to crafting lively digital proposals without deep web coding skills. And they will receive coaching on how to think digitally about how a proposal can be conveyed electronically to the right donor.

Visualization of the small RNA transcriptome using seqclusterViz.

The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson's disease .

The cloud is the limit: A case study of programming on the web, with the web

Abstract The last ten years have seen a proliferation of introductory programming environments for younger learners. Increasingly, these environments are moving into the “cloud” where they can be accessed through web browsers and run on a variety of devices including tablets and smartphones. The shift to online settings enables a variety of powerful pedagogical features to be incorporated into the design of these learning environments, including making it easy to share learner-authored programs, browse projects written by others, and allow learners to incorporate various Internet resources into their work. Further, the Internet itself can serve as a productive canvas upon which novice programmers can create in the form of dynamic and interactive web pages. This shift in venue for authoring and editing programs is particularly well-suited for young learners growing up in an increasingly online world. In this paper, we present theoretical and practical arguments for online introductory programming environments as powerful learning tools and present data showing various ways young learners take advantage of features of the environment enabled by being situated online. In particular, the paper looks at how the online context can support young learners in authoring programs and interacting with programs authored by others. The contribution of this work is to advance our understanding of how the Internet can be utilized as a resource to situate learning and serve as an inviting and accessible pathway into computing.

CCT: a coordinate conversion tool for hepatitis B virus

The hepatitis B virus (HBV) genome has ∼3 200 nucleotides, coding for seven proteins in four overlapping open reading frames (ORFs). Comparison of genomic coordinates between different samples and/or published literature requires manual conversion. An online tool is presented to convert nucleotide or amino acid positions between ORFs, regions and domains of the HBV genome. The user enters a position into an interactive web page, which then shows this position in all other applicable ORFs, regions or domains and plots it on a diagrammatic representation of the HBV genome. This tool assists researchers to convert coordinates, thereby facilitating comparisons between samples.

Geographical mapping of advanced practice registered nurses in Louisiana: Leveraging the power of data display.

Identifying the locations of advanced practice registered nurses (APRNs) in the state is challenging without data readily available, which can adversely affect stakeholder initiatives. The purpose of this project was to develop an online interactive map reflecting distribution of APRNs licensed by the Louisiana State Board of Nursing (LSBN), heightening APRN visibility and improving usability of data for policy, education, practice, and research initiatives. A descriptive design with development of a graphical interactive map showing all Louisiana parishes with integrated distribution summaries of APRNs was made. Work proceeded from paper to higher fidelity simulations to the final interactive web page. Compatibility with LSBN's web page and annual data upload were ensured. The project was done in collaboration with LSBN, an academic institution, and a privately hired web designer. The principals of Louisiana State Board of Nursing approved the final product. The product meets and exceeds the expectations for mapping. Evaluation of use and usability will be done at the discretion of LSBN. The outcome of this project will serve to heighten visibility of the distribution of APRNs in the state of Louisiana, enhancing opportunities for APRNs and for patients. Furthermore, those interested in leveraging the information in policy, education, or research initiatives will be served.

Implementation of Safe City Concept – Procedure of Choosing New Safety Measures

Abstract Over the studies of Smart and Safe City concepts number of solutions increasing the safety and security in cities were identified. However, as every city faces different problems in different circumstances, the same solution will not bring the same results everywhere. Individualistic planning of safety and security enhancements is needed. The aim of this paper is to help with decision-making processes - to identify, which safety and security solutions are the most fitting for the specific situation of the specific city. For this purpose, part of the methodological procedure of implementation of Safe City concept solutions is presented within this paper for discussion. In this paper, I decided to deal with the part of procedure that seems to be the least addressed of them – with decision support for choosing new safety measures for implementation. The whole methodological procedure is to be created within an interactive webpage guide.

Give thanks for a little and you will find a lot: The role of a support seeker’s reply in online support provision

ABSTRACTThis experiment examined reciprocal communication among support seekers and support providers in online support forums. An interactive online support forum web page was employed where comments to a support-seeking post and a support seeker’s reply to previous comments were manipulated, and participants could post their responses on the interactive web page. Results showed that support seekers received more supportive responses from subsequent viewers when they expressed appreciation for earlier comments. Compared with an appreciative reply to supportive comments, the same reply to unsupportive comments elicited more positive expectancy violations and thus higher levels of action-focused supportiveness in viewers’ responses. This study extended the application of expectancy violations theory to the context of online support forums.

PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes

BackgroundBacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionally important. Pan-genomes consist of large amounts of data, which can restrict researchers ability to locate and analyze these regions. Multiple software packages are available to visualize pan-genomes, but currently their ability to address these concerns are limited by using only pre-computed data sets, prioritizing core over variable gene clusters, or by not accounting for pan-chromosome positioning in the viewer.ResultsWe introduce PanACEA (Pan-genome Atlas with Chromosome Explorer and Analyzer), which utilizes locally-computed interactive web-pages to view ordered pan-genome data. It consists of multi-tiered, hierarchical display pages that extend from pan-chromosomes to both core and variable regions to single genes. Regions and genes are functionally annotated to allow for rapid searching and visual identification of regions of interest with the option that user-supplied genomic phylogenies and metadata can be incorporated. PanACEA’s memory and time requirements are within the capacities of standard laptops. The capability of PanACEA as a research tool is demonstrated by highlighting a variable region important in differentiating strains of Enterobacter hormaechei.ConclusionsPanACEA can rapidly translate the results of pan-chromosome programs into an intuitive and interactive visual representation. It will empower researchers to visually explore and identify regions of the pan-chromosome that are most biologically interesting, and to obtain publication quality images of these regions.

Effects of Semi-Finished Products as a Scaffolding on University Liberal Art Students’ Learning of Multimedia Technology and Webpage Producing

This paper presents a study carried out at Beijing Normal University with the aim of investigating whether semi-finished products could affect liberal arts students’ mastery of knowledge, mastery of operational skills and ICT self-efficacy in multimedia creation. The literature has argued that obstacles in creating multimedia artifacts lead liberal arts students to have low ICT self-efficacy. Semi-finished products are used as a scaffolding to facilitate liberal arts students’ creation of multimedia artifacts, such as Flash animations and interactive web-pages. However, empirical research on the effects of such scaffolding is lacking. We conducted a quasi-experiment in which we compared an experimental class of 117 students majoring in History with a control class of 102 students majoring in Chinese Language and Literature who took a Multimedia Technology and Webpage Producing (MTWP) course. The experimental class (revising condition) used semi-finished products to develop animations and web-pages while the control class (creating condition) developed animations and web-pages from scratch. Data were collected through a Knowledge and Skill Test and a Scale on ICT self-efficacy. T-tests were used to compare outcomes of the two conditions. Results revealed that students’ mastery of knowledge in the revising condition was significantly higher than students in the creation condition, but there were no significant differences between the two conditions in terms of students’ mastery of operational skills. Results also showed that there were significant differences between the two conditions in terms of students’ ICT self-efficacy. Further analysis indicated that students’ ICT self-efficacy in the revising condition improved significantly from pre-test to post-test, while those in the creating condition declined, but it was not significant. Implications for ICT teaching in higher education were discussed.

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community.

El uso de las TIC en la formación de conceptos matemáticos

The objective of the research was the modes of action to define concepts with the use of ICT, which favors the development of professional pedagogical skills in students. In particular, it shows the authors' experience in harnessing the potential of ICT for the study of the concept of continuous function in one point, corresponds to the Mathematical Analysis discipline, in the second year of the initial training of the Graduate in Mathematics-Physics Education at the University of Holguin, through the use of an interactive web page created by the second author of this paper. The experience was part of the research carried out by a group of teachers as part of the institutional project related to the initial training of the Graduate in MathematicsPhysics Education at the University of Holguin. The methodology used was based on action research, through the creation and implementation of innovative proposals to use ICT. This has been accomplished from the argumentation of a methodological proposal for the use of ICT and possible alternatives in the classroom, based on the determination of the potentialities and limitations derived from the diagnosis. Through observation, the survey application and the entrance and exit tests are in the understanding of the same. The organization of students by teams or small groups, for the development of classes and the accomplishment of the different tasks interacting with the use of ICT, favored a cooperative learning and communication among students.

Choose Your Own Research Data Management Guidance

The GW4 Research Data Services Group has developed a Research  Data Management Triage Tool to help researchers find answers quickly  to the more common research data queries, and direct them to appropriate guidance and sources of advice for more complex queries.  The tool takes the form of an interactive web page that asks users  questions and updates itself in response. The conversational and  dynamic way the tool progresses is similar to the behaviour of text  adventures, which are a genre of interactive fiction; this is one of the  oldest forms of computer game and was also popular in print form in,  for example,  the Choose Your Own Adventure and Fighting Fantasy  series of books.  In fact, the tool was written using interactive fiction  software.  It was tested with staff and students at the four UK  universities within the GW4 collaboration.

Focusing in on employability: using content analysis to explore the employability discourse in UK and USA universities

In this paper, we have taken initial steps towards highlighting the employability discourse in higher education by using content analysis to explore website data at 40 higher education institutions (HEIs) in the UK and 40 HEIs in the USA by searching for ‘employability’ in respective web engines. The findings from our preliminary data analysis were inserted into a MIT SIMILE software package to create a bespoke, interactive webpage that could be disseminated for discussion by higher education managers. The initial findings suggest that, in the UK, the broad discourse is centred upon government policies and targeted preparation for employment while in the USA it is centred upon the institutional vision and social inclusion agenda. Recent graduates’ views were sought on these initial findings to validate whether their experiences corroborated with our suggested employability discourse claims. These insights are a useful first step for HEIs to question and re-evaluate employability at an institutional level.

USING BLOGS IN TEACHING ENGLISH TO PHILOLOGY STUDENTS

This paper reports on an innovative approach to using blogs in teaching English as a foreign language. A blog is a sound example of information and communication technologies (ICT) implementation for language learning. In this paper, authors present the results of a small-scale action research aimed at analysing students’ perceptions of blogging. In total, 25 first-year university students majoring in English took part in a survey. The research results give the evidence of the benefits of using blogs: it encourages students’ autonomous learning, expands their collaboration through comments and discussions, improves language skills, increases the sense of responsibility and the desire for life-long learning, etc. At the same time, teachers consider blogs to be an effective facilitation for greater learner interaction and skills development. The research deals with the detailed blog starting guide for teachers of English. Authors instruct how to create and maintain blogs, as these interactive web pages prove to be effective for students online chatting, exchanging photos, videos, pictures, thereby expanding their language study beyond the classroom. For those who refuse being involved in the creation of a personal web page, some useful blog links are given. For better understanding of blogging efficiency, the researchers report on the positive implementation of blogs in teaching English, focusing on developing reading, writing, speaking and listening skills.

Internet-based support for self-management strategies for people with COPD–protocol for a controlled pragmatic pilot trial of effectiveness and a process evaluation in primary healthcare

IntroductionThe use of adequate self-management strategies for people with chronic obstructive pulmonary disease (COPD) reduces healthcare use, improves health-related quality of life (HRQoL) and recovery after acute exacerbations. However, not...