Smartphone-Enabled Web-Based Simulation of Cellular Neurophysiology for Laboratory Course and its Effectiveness.

The introduction of computer simulations has enhanced the teaching of neurobiology. Many simulators for personal computers are available, but in countries where schools have low school information and communication technology readiness, it is difficult to introduce computer simulations. Even in such countries, however, students often have their own smartphones and are good at operating them. Therefore, we have developed five web-based simulators that cover a wide range of neurophysiology, including single and whole-cell channel currents, membrane potentials and generation and conduction of action potentials using HTML5 and JavaScript. These simulators may be run free of charge on any device, regardless of the model or OS, thereby enabling schools that have no experience in introducing simulations to introduce them easily. These simulators were especially useful in many schools during COVID-19 restrictions. In this paper, we explain the functions of the simulators we have developed and introduce some practical examples. To verify the usefulness of the simulators, we also conducted a survey in the classrooms in which the simulators were used. Understanding and motivation to learn was shown to increase significantly, indicating that these are useful for neurobiology education.

SpecPad: device-independent NMR data visualization and processing based on the novel DART programming language and Html5 Web technology.

SpecPad is a new device-independent software program for the visualization and processing of one-dimensional and two-dimensional nuclear magnetic resonance (NMR) time domain (FID) and frequency domain (spectrum) data. It is the result of a project to investigate whether the novel programming language DART, in combination with Html5 Web technology, forms a suitable base to write an NMR data evaluation software which runs on modern computing devices such as Android, iOS, and Windows tablets as well as on Windows, Linux, and Mac OS X desktop PCs and notebooks. Another topic of interest is whether this technique also effectively supports the required sophisticated graphical and computational algorithms. SpecPad is device-independent because DART's compiled executable code is JavaScript and can, therefore, be run by the browsers of PCs and tablets. Because of Html5 browser cache technology, SpecPad may be operated off-line. Network access is only required during data import or export, e.g. via a Cloud service, or for software updates. A professional and easy to use graphical user interface consistent across all hardware platforms supports touch screen features on mobile devices for zooming and panning and for NMR-related interactive operations such as phasing, integration, peak picking, or atom assignment. Copyright © 2017 John Wiley & Sons, Ltd.

JavaScript Access to DICOM Network and Objects in Web Browser.

Digital imaging and communications in medicine (DICOM) 3.0 standard provides the baseline for the picture archiving and communication systems (PACS). The development of Internet and various communication media initiated demand for non-DICOM access to PACS systems. Ever-increasing utilization of the web browsers, laptops and handheld devices, as opposed to desktop applications and static organizational computers, lead to development of different web technologies. The DICOM standard officials accepted those subsequently as tools of alternative access. This paper provides an overview of the current state of development of the web access technology to the DICOM repositories. It presents a different approach of using HTML5 features of the web browsers through the JavaScript language and the WebSocket protocol by enabling real-time communication with DICOM repositories. JavaScript DICOM network library, DICOM to WebSocket proxy and a proof-of-concept web application that qualifies as a DICOM 3.0 device were developed.

Exploring HTML5 Package Interactive Content in Supporting Learning Through Self-Paced Massive Open Online Courses on Healthy Aging: Mixed Methods Study.

BACKGROUND: The rapidly aging population and the growth of geriatric medicine in the field of internal medicine are not supported by sufficient gerontological training in many health care disciplines. There is rising awareness about the education and training needed to adequately prepare health care professionals to address the needs of the older adult population. Massive open online courses (MOOCs) might be the best alternative method of learning delivery in this context. However, the diversity of MOOC participants poses a challenge for MOOC providers to innovate in developing learning content that suits the needs and characters of participants. OBJECTIVE: The primary outcome of this study was to explore students' perceptions and acceptance of HTML5 package (H5P) interactive content in self-paced MOOCs and its association with students' characteristics and experience in using MOOCs. METHODS: This study used a cross-sectional design, combining qualitative and quantitative approaches. Participants, predominantly general practitioners from various regions of Indonesia with diverse educational backgrounds and age groups, completed pretests, engaged with H5P interactive content, and participated in forum discussions and posttests. Data were retrieved from the online questionnaire attached to a selected MOOC course. Students' perceptions and acceptance of H5P interactive content were rated on a 6-point Likert scale from 1 (strongly disagree) to 6 (strongly agree). Data were analyzed using SPSS (IBM Corp) to examine demographics, computer literacy, acceptance, and perceptions of H5P interactive content. Quantitative analysis explored correlations, while qualitative analysis identified recurring themes from open-ended survey responses to determine students' perceptions. RESULTS: In total, 184 MOOC participants agreed to participate in the study. Students demonstrated positive perceptions and a high level of acceptance of integrating H5P interactive content within the self-paced MOOC. Analysis of mean (SD) value across all responses consistently revealed favorable scores (greater than 5), ranging from 5.18 (SD 0.861) to 5.45 (SD 0.659) and 5.28 (SD 0.728) to 5.52 (SD 0.627), respectively. This finding underscores widespread satisfaction and robust acceptance of H5P interactive content. Students found the H5P interactive content more satisfying and fun, easier to understand, more effective, and more helpful in improving learning outcomes than material in the form of common documents and learning videos. There is a significant correlation between computer literacy, students' acceptance, and students' perceptions. CONCLUSIONS: Students from various backgrounds showed a high level of acceptance and positive perceptions of leveraging H5P interactive content in the self-paced MOOC. The findings suggest potential new uses of H5P interactive content in MOOCs, such as interactive videos with pop-up questions, to substitute for synchronous learning. The study underscores the significance of tailored educational strategies in supporting the professional development of health care professionals.

Subtitle synchronization across multiple screens and devices.

Ambient Intelligence is a new paradigm in which environments are sensitive and responsive to the presence of people. This is having an increasing importance in multimedia applications, which frequently rely on sensors to provide useful information to the user. In this context, multimedia applications must adapt and personalize both content and interfaces in order to reach acceptable levels of context-specific quality of service for the user, and enable the content to be available anywhere and at any time. The next step is to make content available to everybody in order to overcome the existing access barriers to content for users with specific needs, or else to adapt to different platforms, hence making content fully usable and accessible. Appropriate access to video content, for instance, is not always possible due to the technical limitations of traditional video packaging, transmission and presentation. This restricts the flexibility of subtitles and audio-descriptions to be adapted to different devices, contexts and users. New Web standards built around HTML5 enable more featured applications with better adaptation and personalization facilities, and thus would seem more suitable for accessible AmI environments. This work presents a video subtitling system that enables the customization, adaptation and synchronization of subtitles across different devices and multiple screens. The benefits of HTML5 applications for building the solution are analyzed along with their current platform support. Moreover, examples of the use of the application in three different cases are presented. Finally, the user experience of the solution is evaluated.

3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal.

BACKGROUND: The increasing number of organic and inorganic structures promotes the development of the "Big Data" in chemistry and material science, and raises the need for cross-platform and web-based methods to search, view and edit structures. Many web-based three-dimensional (3D) structure tools have been developed for displaying existing models, building new models, and preparing initial input files for external calculations. But few of these tools can deal with crystal structures. RESULTS: We developed a user-friendly and versatile program based on standard web techniques, such as Hyper Text Markup Language 5 (HTML5), Cascade Style Sheet (CSS) and JavaScript. Both non-periodic organic molecule and crystal structure can be visualized, built and edited interactively. The atom, bond, angle and dihedral in a molecule can be viewed and modified using sample mouse operations. A wide range of cheminformatics algorithms for crystal structure are provided, including cleaving surfaces, establishing vacuum layers, and building supercells. Four displayed styles, namely "Primitive cell", "Original", "In-cell" and "Packing" can be used to visualize a unit cell. Additionally, the initial input files for Vienna Ab-initio Simulation Package (VASP) and Gaussian can be obtained by interacting with dialog boxes in 3DStructGen. CONCLUSIONS: 3DStructGen is a highly platform-independent program. It can provide web service independently or can be integrated into other web platforms. Other than local desktop software, it does not require any additional effort to install the system but a web browser supporting HTML5. 3DStructGen may play a valuable role in online chemistry education and pre-processing of quantum calculations. The program has been released under MIT open-source license and is available on: https://matgen.nscc-gz.cn/Tools.html.

OpenMX Viewer: A web-based crystalline and molecular graphical user interface program.

The OpenMX Viewer (Open source package for Material eXplorer Viewer) is a web-based graphical user interface (GUI) program for visualization and analysis of crystalline and molecular structures and 3D grid data in the Gaussian cube format such as electron density and molecular orbitals. The web-based GUI program enables us to quickly visualize crystalline and molecular structures by dragging and dropping XYZ, CIF, or OpenMX input/output files, and analyze static/dynamic structural properties conveniently in a web browser. Several basic functionalities such as analysis of Mulliken charges, molecular dynamics, geometry optimization and band structure are included. In addition, based on marching cubes, marching tetrahedra and surface nets algorithms with Affine transformation, 3D isosurface techniques are supported to visualize electron density and molecular/crystalline orbitals in the cube format with superposition of a crystalline or molecular structure. Furthermore, the Band Structure Viewer is implemented for showing a band structure in a web browser. By accessing the website of the OpenMX Viewer, the latest OpenMX Viewer is always available for users to visualize various structures and analyze their properties without installations, upgrades, updates, registration, sign-in and terminal commands.

Programming languages in chemistry: a review of HTML5/JavaScript.

This is one part of a series of reviews concerning the application of programming languages in chemistry, edited by Dr. Rajarshi Guha. This article reviews the JavaScript technology as it applies to the chemistry discipline. A discussion of the history, scope and technical details of the programming language is presented.

Implementing WebGL and HTML5 in Macromolecular Visualization and Modern Computer-Aided Drug Design.

Web browsers have long been recognized as potential platforms for remote macromolecule visualization. However, the difficulty in transferring large-scale data to clients and the lack of native support for hardware-accelerated applications in the local browser undermine the feasibility of such utilities. With the introduction of WebGL and HTML5 technologies in recent years, it is now possible to exploit the power of a graphics-processing unit (GPU) from a browser without any third-party plugin. Many new tools have been developed for biological molecule visualization and modern drug discovery. In contrast to traditional offline tools, real-time computing, interactive data analysis, and cross-platform analyses feature WebGL- and HTML5-based tools, facilitating biological research in a more efficient and user-friendly way.

The WebACS - An Accessible Graphical Editor.

This paper is about the solution to accessibility problems met when implementing a graphical editor, a major challenge being the comprehension of the relationships between graphical components, which needs to be guaranteed for blind and vision impaired users. In the concrete case the HTML5 canvas and Javascript were used. Accessibility was reached by implementing a list view of elements, which also enhances the usability of the editor.

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization.

In this paper we present a web-based software solution to the problem of implementing real-time collaborative neuroimage visualization. In both clinical and research settings, simple and powerful access to imaging technologies across multiple devices is becoming increasingly useful. Prior technical solutions have used a server-side rendering and push-to-client model wherein only the server has the full image dataset. We propose a rich client solution in which each client has all the data and uses the Google Drive Realtime API for state synchronization. We have developed a small set of reusable client-side object-oriented JavaScript modules that make use of the XTK toolkit, a popular open-source JavaScript library also developed by our team, for the in-browser rendering and visualization of brain image volumes. Efficient realtime communication among the remote instances is achieved by using just a small JSON object, comprising a representation of the XTK image renderers' state, as the Google Drive Realtime collaborative data model. The developed open-source JavaScript modules have already been instantiated in a web-app called MedView, a distributed collaborative neuroimage visualization application that is delivered to the users over the web without requiring the installation of any extra software or browser plugin. This responsive application allows multiple physically distant physicians or researchers to cooperate in real time to reach a diagnosis or scientific conclusion. It also serves as a proof of concept for the capabilities of the presented technological solution.

MuffinInfo: HTML5-Based Statistics Extractor from Next-Generation Sequencing Data.

Usually, the information known a priori about a newly sequenced organism is limited. Even resequencing the same organism can generate unpredictable output. We introduce MuffinInfo, a FastQ/Fasta/SAM information extractor implemented in HTML5 capable of offering insights into next-generation sequencing (NGS) data. Our new tool can run on any software or hardware environment, in command line or graphically, and in browser or standalone. It presents information such as average length, base distribution, quality scores distribution, k-mer histogram, and homopolymers analysis. MuffinInfo improves upon the existing extractors by adding the ability to save and then reload the results obtained after a run as a navigable file (also supporting saving pictures of the charts), by supporting custom statistics implemented by the user, and by offering user-adjustable parameters involved in the processing, all in one software. At the moment, the extractor works with all base space technologies such as Illumina, Roche, Ion Torrent, Pacific Biosciences, and Oxford Nanopore. Owing to HTML5, our software demonstrates the readiness of web technologies for mild intensive tasks encountered in bioinformatics.

WebAL Comes of Age: A Review of the First 21 Years of Artificial Life on the Web.

We present a survey of the first 21 years of web-based artificial life (WebAL) research and applications, broadly construed to include the many different ways in which artificial life and web technologies might intersect. Our survey covers the period from 1994-when the first WebAL work appeared-up to the present day, together with a brief discussion of relevant precursors. We examine recent projects, from 2010-2015, in greater detail in order to highlight the current state of the art. We follow the survey with a discussion of common themes and methodologies that can be observed in recent work and identify a number of likely directions for future work in this exciting area.

Avatar Web-Based Self-Report Survey System Technology for Public Health Research: Technical Outcome Results and Lessons Learned.

This paper reports on a specific Web-based self-report data collection system that was developed for a public health research study in the United States. Our focus is on technical outcome results and lessons learned that may be useful to other projects requiring such a solution. The system was accessible from any device that had a browser that supported HTML5. Report findings include: which hardware devices, Web browsers, and operating systems were used; the rate of survey completion; and key considerations for employing Web-based surveys in a clinical trial setting.

Empirical evaluation of a virtual laboratory approach to teach lactate dehydrogenase enzyme kinetics.

BACKGROUND: Personalised instruction is increasingly recognised as crucial for efficacious learning today. Our seminal work delineates and elaborates on the principles, development and implementation of a specially-designed adaptive, virtual laboratory. AIMS: We strived to teach laboratory skills associated with lactate dehydrogenase (LDH) enzyme kinetics to 2nd-year biochemistry students using our adaptive learning platform. Pertinent specific aims were to:(1)design/implement a web-based lesson to teach lactate dehydrogenase(LDH) enzyme kinetics to 2nd-year biochemistry students(2)determine its efficacious in improving students' comprehension of enzyme kinetics(3)assess their perception of its usefulness/manageability(vLab versus Conventional Tutorial). METHODS: Our tools were designed using HTML5 technology. We hosted the program on an adaptive e-learning platform (AeLP). Provisions were made to interactively impart informed laboratory skills associated with measuring LDH enzyme kinetics. A series of e-learning methods were created. Tutorials were generated for interactive teaching and assessment. RESULTS: The learning outcomes herein were on par with that from a conventional classroom tutorial. Student feedback showed that the majority of students found the vLab learning experience "valuable"; and the vLab format/interface "well-designed". However, there were a few technical issues with the 1st roll-out of the platform. CONCLUSIONS: Our pioneering effort resulted in productive learning with the vLab, with parity with that from a conventional tutorial. Our contingent discussion emphasises not only the cornerstone advantages, but also the shortcomings of the AeLP method utilised. We conclude with an astute analysis of possible extensions and applications of our methodology.

ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics.

ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.Graphical abstractAdd interactive 2D and 3D chemical sketchers, graphics, and spectra to websites and apps with ChemDoodle Web Components.

BrainBrowser: distributed, web-based neurological data visualization.

Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used to analyze them have, in response, become more collaborative and exploratory. Tools and infrastructure are continuously being developed and deployed to facilitate research in this context: grid computation platforms to process the data, distributed data stores to house and share them, high-speed networks to move them around and collaborative, often web-based, platforms to provide access to and sometimes manage the entire system. BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. BrainBrowser leverages modern web technologies, such as WebGL, HTML5 and Web Workers, to visualize 3D surface and volumetric neuroimaging data in any modern web browser without requiring any browser plugins. It is thus trivial to integrate BrainBrowser into any web-based platform. BrainBrowser is simple enough to produce a basic web-based visualization in a few lines of code, while at the same time being robust enough to create full-featured visualization applications. BrainBrowser can dynamically load the data required for a given visualization, so no network bandwidth needs to be waisted on data that will not be used. BrainBrowser's integration into the standardized web platform also allows users to consider using 3D data visualization in novel ways, such as for data distribution, data sharing and dynamic online publications. BrainBrowser is already being used in two major online platforms, CBRAIN and LORIS, and has been used to make the 1TB MACACC dataset openly accessible.

Web-based, mobile-device friendly, self-report survey system incorporating avatars and gaming console techniques.

We describe building an avatar-based self-report data collection tool to be used for a specific HIV prevention research project that is evaluating the feasibility and acceptability of this novel approach to collect self-reported data among youth. We discuss the gathering of requirements, the process of building a prototype of the envisioned system, and the lessons learned during the development of the solution. Specific knowledge is shared regarding technical experience with software development technologies and possible avenues for changes that could be considered if such a self-report survey system is used again. Examples of other gaming and avatar technology systems are included to provide further background.

Transforming clinical imaging and 3D data for virtual reality learning objects: HTML5 and mobile devices implementation.

Web deployable anatomical simulations or "virtual reality learning objects" can easily be produced with QuickTime VR software, but their use for online and mobile learning is being limited by the declining support for web browser plug-ins for personal computers and unavailability on popular mobile devices like Apple iPad and Android tablets. This article describes complementary methods for creating comparable, multiplatform VR learning objects in the new HTML5 standard format, circumventing platform-specific limitations imposed by the QuickTime VR multimedia file format. Multiple types or "dimensions" of anatomical information can be embedded in such learning objects, supporting different kinds of online learning applications, including interactive atlases, examination questions, and complex, multi-structure presentations. Such HTML5 VR learning objects are usable on new mobile devices that do not support QuickTime VR, as well as on personal computers. Furthermore, HTML5 VR learning objects can be embedded in "ebook" document files, supporting the development of new types of electronic textbooks on mobile devices that are increasingly popular and self-adopted for mobile learning.