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This report presents the findings of a project from the 8th Biomedical Linked Annotation Hackathon (BLAH) to explore lightweight technology stacks to enhance assistive linked annotations. Using modern JavaScript frameworks and edge functions, in-browser Named Entity Recognition (NER), serverless embedding and vector search within web interfaces, and efficient serverless full-text search were implemented. Through this experimental approach, a proof of concept to demonstrate the feasibility and performance of these technologies was demonstrated. The results show that lightweight stacks can significantly improve the efficiency and cost-effectiveness of annotation tools and provide a local-first, privacy-oriented, and secure alternative to traditional server-based solutions in various use cases. This work emphasizes the potential of developing annotation interfaces that are more responsive, scalable, and user-friendly, which would benefit bioinformatics researchers, practitioners, and software developers., (© 2024. The Author(s).)

There is an increasing number of libraries devoted to parsing, manipulating and visualising phylogenetic trees in JavaScript. Many of these libraries bundle tree manipulation with visualisation, but have limited ability to manipulate trees and lack detailed documentation. As the number of web-based phylogenetic tools and the size of phylogenetics datasets increases, there is a need for a library that parses, writes and manipulates phylogenetic trees that is interoperable with other phylogenetic and data visualisation libraries. Here we introduce PhyloJS, a light zero-dependency TypeScript and JavaScript library for reading, writing and manipulating phylogenetic trees. PhyloJS allows for modification of and data-extraction from trees to integrate with other phylogenetics and data visualisation libraries. It can swiftly handle large trees, up to at least 10 6 tips in size, making it ideal for developing the next generation of more complex web-based phylogenetics applications handling ever larger datasets. The PhyloJS source code is available on GitHub (https://github.com/clockor2/phylojs) and can be installed via npm with the command npm install phylojs. Extensive documentation is available at https://clockor2.github.io/phylojs/., Competing Interests: LAF and WW declare no conflicts of interest., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)

The present tutorial provides a technical overview of how to create web applications for online psychological experiments from scratch via the HTML/CSS/JavaScript framework. This approach allows virtually unlimited flexibility in accomplishing anything in an online experiment that a regular computer (or smartphone, etc.) is capable of. Apart from offering a fast introduction for complete beginners, this tutorial may also serve as a helpful guideline for more experienced programmers and researchers. Connected to the tutorial, a specific implementation is also given via the free and open-source template project at https://github.com/gasparl/expapp , intended to be improved by the community to always follow the latest technological advancements and general good practices., (© 2023. The Author(s).)

Mean circulatory filling pressure, venous return curve, and Guyton's graphical analysis are basic concepts in cardiovascular physiology. However, some medical students may not know how to view and interpret or understand them adequately. To deepen students' understanding of the graphical analysis, in place of having to perform live animal experiments, we developed an interactive cardiovascular simulator, as a self-learning tool, as a web application. The minimum closed-loop model consisted of a ventricle, an artery, resistance, and a vein, excluding venous resistance. The simulator consists of three modules: setting (parameters and simulation modes), calculation, and presentation. In the setting module, the user can interactively customize model parameters, compliances, resistance, Emax of the ventricular contractility, total blood volume, and unstressed volume. The hemodynamics are calculated in three phases: filling (late diastole), ejection (systole), and flow (early diastole). In response to the user's settings, the simulator graphically presents the hemodynamics: the pressure-volume relations of the artery, vein, and ventricle, the venous return curves, and the stroke volume curves. The mean filling pressure is calculated at approximately 7 mmHg at the initial setting. The venous return curves, linear and concave, are dependent on the venous compliance. The hemodynamic equilibrium point is marked on the crossing point of venous return curve and the stroke volume curve. Users can interactively do discovery learning, and try and confirm their interests and get their questions answered about hemodynamic concepts by using the simulator., (© 2024. The Author(s).)

Object-oriented programming (OOP) embodies a software development paradigm grounded in representing real-world entities as objects, facilitating a more efficient and structured modelling approach. In this article, we explore the synergy between OOP principles and the TypeScript (TS) programming language to create a JSON-formatted database designed for storing arrays of biological features. This fusion of technologies fosters a controlled and modular code script, streamlining the integration, manipulation, expansion, and analysis of biological data, all while enhancing syntax for improved human readability, such as through the use of dot notation. We advocate for biologists to embrace Git technology, akin to the practices of programmers and coders, for initiating versioned and collaborative projects. Leveraging the widely accessible and acclaimed IDE, Visual Studio Code, provides an additional advantage. Not only does it support running a Node.js environment, which is essential for running TS, but it also efficiently manages GitHub versioning. We provide a use case involving taxonomic data structure, focusing on angiosperm legume plants. This method is characterized by its simplicity, as the tools employed are both fully accessible and free of charge, and it is widely adopted by communities of professional programmers. Moreover, we are dedicated to facilitating practical implementation and comprehension through a comprehensive tutorial, a readily available pre-built database at GitHub, and a new package at npm., (© The Author(s) 2024. Published by Oxford University Press.)

Viruses that infect as well as often kill bacteria are called bacteriophages, or phages. Because of their ability to act bactericidally, phages increasingly are being employed clinically as antibacterial agents, an infection-fighting strategy that has been in practice now for over one hundred years. As with antibacterial agents generally, the development as well as practice of this phage therapy can be aided via the application of various quantitative frameworks. Therefore, reviewed here are considerations of phage multiplicity of infection, bacterial likelihood of becoming adsorbed as a function of phage titers, bacterial susceptibility to phages also as a function of phage titers, and the use of Poisson distributions to predict phage impacts on bacteria. Considered in addition is the use of simulations that can take into account both phage and bacterial replication. These various approaches can be automated, i.e., by employing a number of online-available apps provided by the author, the use of which this review emphasizes. In short, the practice of phage therapy can be aided by various mathematical approaches whose implementation can be eased via online automation.

Background: Exploring metagenomic contigs and "binning" them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure., Results: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena's usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset., Conclusions: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena , together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data. Video Abstract., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Conversational User Interfaces (CUI) are widely used, with about 1.8 billion users worldwide in 2020. For designing and building CUI, dialogue designers have to decide on how the CUI communicates with users and what dialogue strategies to pursue (e.g. reactive vs. proactive). Dialogue strategies can be evaluated in user tests by comparing user perceptions and reactions to different dialogue strategies. Simulating CUI and running them online, for example on crowdsourcing websites, is an attractive avenue to collecting user perceptions and reactions, as they can be gathered time- and cost-effectively. However, developing and deploying a CUI on a crowd sourcing platform can be laborious and requires technical proficiency from researchers. We present Chatbot Language (CBL) as a framework to quickly develop and deploy CUI on crowd sourcing platforms, without requiring a technical background. CBL is a library with specialized CUI functionality, which is based on the high-level language JavaScript. In addition, CBL provides scripts that use the API of the crowd sourcing platform Mechanical Turk (MT) in order to (a) create MT Human Intelligence Tasks (HITs) and (b) retrieve the results of those HITs. We used CBL to run experiments on MT and present a sample workflow as well as an example experiment. CBL is freely available and we discuss how CBL can be used now and may be further developed in the future., (© 2022. The Author(s).)

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., (Copyright © 2023 Faculty for Undergraduate Neuroscience.)

Conducting research via the Internet is a formidable and ever-increasingly popular option for behavioral scientists. However, it is widely acknowledged that web-browsers are not optimized for research: In particular, the timing of display changes (e.g., a stimulus appearing on the screen), still leaves room for improvement. So far, the typically recommended best (or least bad) timing method has been a single (RAF) JavaScript function call within which one would give the display command and obtain the time of that display change. In our Study 1, we assessed two alternatives: Calling the RAF twice consecutively, or calling the RAF during a continually ongoing independent loop of recursive RAF calls. While the former has shown little or no improvement as compared to single RAF calls, with the latter we significantly and substantially improved overall precision, and achieved practically faultless precision in most practical cases. Our two basic methods for effecting display changes, plain text change and color filling, proved equally efficient. In Study 2, we reassessed the "RAF loop" timing method with image elements in combination with three different display methods: We found that the precision remained high when using either or changes - while drawing on a element consistently led to comparatively lower precision. We recommend the "RAF loop" display timing method for improved precision in future studies, and or changes when using image stimuli. We publicly share the easy-to-use code for this method, exactly as employed in our studies., (© 2022. The Psychonomic Society, Inc.)

Recently, WebGL has been widely used in numerous web-based medical image viewers to present advanced imaging visualization. However, in the scenario of medical imaging, there are many challenges of computation time and memory consumption that limit the use of advanced image renderings, such as volume rendering and multiplanar reformation/reconstruction, in low-cost mobile devices. In this study, we propose a client-side rendering low-cost computation algorithm for common two- and three-dimensional medical imaging visualization implemented by pure JavaScript. Particularly, we used the functions of cascading style sheet transform and combinate with Digital Imaging and Communications in Medicine (DICOM)-related imaging to replace the application programming interface with high computation to reduce the computation time and save memory consumption while launching medical imaging interpretation on web browsers. The results show the proposed algorithm significantly reduced the consumption of central and graphics processing units on various web browsers. The proposed algorithm was implemented in an open-source web-based DICOM viewer BlueLight; the results show that it has sufficient rendering performance to display 3D medical images with DICOM-compliant annotations and has the ability to connect to image archive via DICOMweb as well.Keywords: WebGL, DICOMweb, Multiplanar reconstruction, Volume rendering, DICOM, JavaScript, Zero-footprint., (© 2022. The Author(s) under exclusive licence to Society for Imaging Informatics in Medicine.)

The urgent need to protect user privacy and security has emerged as the World Wide Web has become an increasingly necessary part of daily life. Browser fingerprinting is a very interesting topic in the industry of technology security. New technology will always raise new security issues and browser fingerprinting will undoubtedly follow the same process. It has become one of the most popular topics in online privacy because, to date, there is still no exact solution as to how to stop it entirely. The majority of solutions just aim to reduce the likelihood of obtaining a browser fingerprint. Research on browser fingerprinting is unquestionably required since it is essential to educate users, developers, policymakers, and law enforcement about it so that they can make strategic choices based on knowledge. Browser fingerprinting must be recognised in order to defend against privacy problems. A browser fingerprint is described as data gathered by the receiving server to identify a distant device, and it is different from cookies. Websites frequently utilize browser fingerprinting to obtain information about the type and version of the browser, as well as the operating system, and other current settings. It has been known that even when cookies are disabled, fingerprints can be used to fully or partially identify users or devices. In this communication paper, a new insight into the challenge of browser fingerprint is encouraged as a new venture. Thus, the initial way to truly understand the browser fingerprint is the need to collect browser fingerprints. In this work, the process of data collection for browser fingerprinting through scripting, to offer a complete all-in-one fingerprinting test suite, has been thoughtfully divided into appropriate sections and grouped with key information to be carried out. The objective is to gather fingerprint data with no personal identification information and make it an open source of raw datasets in the industry for any future research purposes. To our best knowledge, there are no open datasets made available for browser fingerprints in the research field. The dataset will be widely accessible by anyone interested in obtaining those data. The dataset collected will be very raw and will be in the form of a text file. Thus, the main contribution of this work is to share an open dataset of browser fingerprints along with its collection methodology.

JavaScript Web applications are a common product in industry. As with most applications, Web applications can acquire software flaws (known as bugs), whose symptoms are seen during the development stage and, even worse, in production. The use of debuggers is beneficial for detecting bugs. Unfortunately, most JavaScript debuggers (1) only support the "step into/through" feature in an execution program to detect a bug, and (2) do not allow developers to go back-in-time at the application execution to take actions to detect the bug accurately. For example, the second limitation does not allow developers to modify the value of a variable to fix a bug while the application is running or test if the same bug is triggered with other values of that variable. Using concepts such as continuations and static analysis, this article presents a usable debugger for JavaScript, named DeloreanJS, which enables developers to go back-in-time in different execution points and resume the execution of a Web application to improve the understanding of a bug, or even experiment with hypothetical scenarios around the bug. Using an online and available version, we illustrate the benefits of DeloreanJS through five examples of bugs in JavaScript. Although DeloreanJS is developed for JavaScript, a dynamic prototype-based object model with side effects (mutable variables), we discuss our proposal with the state-of-art/practice of debuggers in terms of features. For example, modern browsers like Mozilla Firefox include a debugger in their distribution that only support for the breakpoint feature. However DeloreanJS uses a graphical user interface that considers back-in-time features. The aim of this study is to evaluate and compare the usability of DeloreanJS and Mozilla Firefox's debugger using the system usability scale approach. We requested 30 undergraduate students from two computer science programs to solve five tasks. Among the findings, we highlight two results. First, we found that 100% (15) of participants recommended DeloreanJS, and only 53% (eight) recommended Firefox's debugger to complete the tasks. Second, whereas the average score for DeloreanJS is 71.6 ("Good"), the average score for Firefox's debugger is 55.8 ("Acceptable")., Competing Interests: The authors declare there are no competing interests., (©2023 Leger et al.)

Here we describe a JavaScript toolbox to perform online rating studies with auditory material. The main feature of the toolbox is that audio samples are associated with visual tokens on the screen that control audio playback and can be manipulated depending on the type of rating. This allows the collection of single- and multidimensional feature ratings, as well as categorical and similarity ratings. The toolbox ( github.com/pwdonh/audio_tokens ) can be used via a plugin for the widely used jsPsych, as well as using plain JavaScript for custom applications. We expect the toolbox to be useful in psychological research on speech and music perception, as well as for the curation and annotation of datasets in machine learning., (© 2022. The Author(s).)

Background: Only a small number of apps addressing allergic rhinitis (AR) patients have been evaluated. This makes their selection difficult. We aimed to introduce a new approach to market research for AR apps, based on the automatic screening of Apple App and Google Play stores., Methods: A JavaScript programme was devised for automatic app screening, and applied in a market assessment of AR self-management apps. We searched the Google Play and Apple App stores of three countries (USA, UK and Australia) with the following search terms: "hay fever", "hayfever", "asthma", "rhinitis", "allergic rhinitis". Apps were eligible if symptoms were evaluated. Results obtained with the automatic programme were compared to those of a blinded manual search. As an example, we used the search to assess apps that can be used to design a combined medication score for AR., Results: The automatic search programme identified 39 potentially eligible apps out of a total of 1593 retrieved apps. Each of the 39 apps was individually checked, with 20 being classified as relevant. The manual search identified 19 relevant apps (out of 6750 screened apps). Combining both methods, a total of 21 relevant apps were identified, pointing to a sensitivity of 95% and a specificity of 99% for the automatic method. Among these 21 apps, only two could be used for the combined symptom-medication score for AR., Conclusions: The programmed algorithm presented herein is able to continuously retrieve all relevant AR apps in the Apple App and Google Play stores, with high sensitivity and specificity. This approach has the potential to unveil the gaps and unmet needs of the apps developed so far., (© 2022 The Authors. Clinical & Experimental Allergy published by John Wiley & Sons Ltd.)

Psychological research is increasingly moving online, where web-based studies allow for data collection at scale. Behavioural researchers are well supported by existing tools for participant recruitment, and for building and running experiments with decent timing. However, not all techniques are portable to the Internet: While eye tracking works in tightly controlled lab conditions, webcam-based eye tracking suffers from high attrition and poorer quality due to basic limitations like webcam availability, poor image quality, and reflections on glasses and the cornea. Here we present MouseView.js, an alternative to eye tracking that can be employed in web-based research. Inspired by the visual system, MouseView.js blurs the display to mimic peripheral vision, but allows participants to move a sharp aperture that is roughly the size of the fovea. Like eye gaze, the aperture can be directed to fixate on stimuli of interest. We validated MouseView.js in an online replication (N = 165) of an established free viewing task (N = 83 existing eye-tracking datasets), and in an in-lab direct comparison with eye tracking in the same participants (N = 50). Mouseview.js proved as reliable as gaze, and produced the same pattern of dwell time results. In addition, dwell time differences from MouseView.js and from eye tracking correlated highly, and related to self-report measures in similar ways. The tool is open-source, implemented in JavaScript, and usable as a standalone library, or within Gorilla, jsPsych, and PsychoJS. In sum, MouseView.js is a freely available instrument for attention-tracking that is both reliable and valid, and that can replace eye tracking in certain web-based psychological experiments., (© 2021. The Author(s).)

Large-scale biodiversity data, for example, on species distribution and richness information, are being mobilized and becoming available at an increasing rate. Interactive web applications like atlases have been developed to visualize available datasets and make them accessible to a wider audience. Web mapping tools are changing rapidly, and different underlying concepts have been developed to visualize datasets at a high cartographic standard.Here, we introduce the Combined Atlas Framework for the development of interactive web atlases for ecological data visualization. We combine two existing approaches: the five stages of the user-centred design approach for web mapping applications and the three U approach for interface success.Subsequently, we illustrate the use of this framework by developing the Atlas of Plant Invasions based on the Global Naturalized Alien Flora (GloNAF) database. This case study illustrates how the newly developed Combined Atlas Framework with a user-centred design philosophy can generate measurable success through communication with the target user group, iterative prototyping and competitive analysis of other existing web mapping approaches.The framework is useful in creating an atlas that employs user feedback to determine usability and utility features within an interactive atlas system. Finally, this framework will enable a better-informed development process of future visualization and dissemination of biodiversity data through web mapping applications and interactive atlases., Competing Interests: The authors have no conflict of interest to declare., (© 2022 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society.)

Web-based data collection is increasingly popular in both experimental and survey-based research because it is flexible, efficient, and location-independent. While dedicated software for laboratory-based experimentation and online surveys is commonplace, researchers looking to implement experiments in the browser have, heretofore, often had to manually construct their studies' content and logic using code. We introduce lab.js, a free, open-source experiment builder that makes it easy to build studies for both online and in-laboratory data collection. Through its visual interface, stimuli can be designed and combined into a study without programming, though studies' appearance and behavior can be fully customized using HTML, CSS, and JavaScript code if required. Presentation and response times are kept and measured with high accuracy and precision heretofore unmatched in browser-based studies. Experiments constructed with lab.js can be run directly on a local computer and published online with ease, with direct deployment to cloud hosting, export to web servers, and integration with popular data collection platforms. Studies can also be shared in an editable format, archived, re-used and adapted, enabling effortless, transparent replications, and thus facilitating open, cumulative science. The software is provided free of charge under an open-source license; further information, code, and extensive documentation are available from https://lab.js.org/ ., (© 2021. The Author(s).)

Voltage-gated sodium channels (Nav) are membrane proteins essential to initiating and propagating action potential in neurons and other excitable cells. For a given organism there are often multiple, specialized sodium channels found in different tissues, whose mutations can cause deleterious effects observed in numerous diseases. Consequently, there is high medical and pharmacological interest in these proteins. Scientific literature often uses membrane diagrams to depict important patterns in these channels including the six transmembrane segments (S1-S6) present in four different homologous domains (D1-D4), the S4 voltage sensors, the pore-lining residue segments and the ion selectivity filter residues, glycosylation and phosphorylation residues, toxin binding sites and the inactivation loop, among others. Most of these diagrams are illustrated either digitally or by hand and programs specifically dedicated to the interactive and data-friendly generation of such visualizations are scarce or non-existing. This paper describes Naview, an open-source javascript visualization compatible with modern web browsers for the dynamic drawing and annotation of voltage-gated sodium channels membrane diagrams based on the D3.js library. By using a graphical user interface and combining user-defined annotations with optional UniProt code as inputs, Naview allows the creation and customization of membrane diagrams. In this interface, a user can also map and display important sodium channel properties, residues, regions and their relationships through symbols, colors, and edge connections. Such features can facilitate data exploration and provide fast, high-quality publication-ready graphics for this highly active area of research., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Afonso, da Fonseca Júnior, Miranda and Bleicher.)

Background: The impact of medical-grade wearable electrocardiographic (ECG) recording technology is increasing rapidly. A wide range of different portable smartphone-connected ECG and heart rate trackers is available on the market. Smart ECG devices are especially valuable to monitor either supraventricular arrhythmias or prolonged QT intervals to avoid drug-induced life-threatening arrhythmias. However, frequent false alarms or false-positive arrhythmia results from wearable devices are unwanted. Therefore, for clinical evaluation, it should be possible to measure and evaluate the biosignals of the wearables independent of the manufacturer., Objective: Unlike radiological devices that do support the universal digital imaging and communications in medicine standard, these medical-grade devices do not yet support a secure standardized exchange pathway between sensors, smartphones/smartwatches, and end services such as cloud storage or universal Web-based application programming interface (API) access. Consequently, postprocessing of recorded ECGs or heart rate interval data requires a whole toolbox of customized software technologies., Methods/results: Various methods for measuring and analyzing nonstandardized ECG and heart rate data are proposed, including online measurement of ECG waveforms within a PDF, access to data using manufacturer-specific software development kits, and access to biosignals using modern Web APIs., Conclusion: With the appropriate workaround, modern software technologies such as JavaScript and PHP allow health care providers and researchers to easily and instantly access necessary and important signal measurements on demand., (© 2021 Heart Rhythm Society.)

Phage therapy is the use of bacterial viruses as antibacterial agents. A primary consideration for commercial development of phages for phage therapy is the number of different bacterial strains that are successfully targeted, as this defines the breadth of a phage cocktail's spectrum of activity. Alternatively, phage cocktails may be used to reduce the potential for bacteria to evolve phage resistance. This, as we consider here, is in part a function of a cocktail's 'depth' of activity. Improved cocktail depth is achieved through inclusion of at least two phages able to infect a single bacterial strain, especially two phages against which bacterial mutation to cross resistance is relatively rare. Here, we consider the breadth of activity of phage cocktails while taking both depth of activity and bacterial mutation to cross resistance into account. This is done by building on familiar algorithms normally used for determination solely of phage cocktail breadth of activity. We show in particular how phage cocktails for phage therapy may be rationally designed toward enhancing the number of bacteria impacted while also reducing the potential for a subset of those bacteria to evolve phage resistance, all as based on previously determined phage properties.

NDEx, the Network Data Exchange (https://www.ndexbio.org) is a web-based resource where users can find, store, share and publish network models of any type and size. NDEx is integrated with Cytoscape, the widely used desktop application for network analysis and visualization. NDEx and Cytoscape are the pillars of the Cytoscape Ecosystem, a diverse environment of resources, tools, applications and services for network biology workflows. In this article, we introduce researchers to NDEx and highlight how it can simplify common tasks in network biology workflows as well as streamline publication and access to). Finally, we show how NDEx can be used programmatically via Python with the 'ndex2' client library, and point readers to additional examples for other popular programming languages such as JavaScript and R. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Getting started with NDEx Basic Protocol 2: Using NDEx and Cytoscape in a publication-oriented workflow Basic Protocol 3: Manipulating networks in NDEx via Python., (© 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.)

Pseudonymization plays a vital role in medical research. In Germany, the Technologie- und Methodenplattform für die vernetzte medizinische Forschung e.V. (TMF) has developed guidelines on how to create pseudonyms and how to handle personally identifiable information (PII) during this process. An open-source implementation of a pseudonymization service following these guidelines and therefore recommended by the TMF is the so-called "Mainzelliste". This web application supports a REST-API for (de-) pseudonymization. For security reasons, a complex session and tokening mechanism for each (de-) pseudonymization is required and a careful interaction between front- and backend to ensure a correct handling of PII. The objective of this work is the development of a library to simplify the integration and usage of the Mainzelliste's API in a TMF conform way. The frontend library uses JavaScript while the backend component is based on Java with an optional Spring Boot extension. The library is available under MIT open-source license from https://github.com/DanielPreciado-Marquez/MainzelHandler.

Objective: The objective of this study is to describe the algorithm and technical implementation of a mobile app that uses adaptive testing to assess an efficient mobile app for the diagnosis of delirium., Materials and Methods: The app was used as part of a NIH-funded project to assess the feasibility, effectiveness, administration time, and costs of the 2-step delirium identification protocol when performed by physicians and nurses, and certified nursing assistants (CNA). The cohort included 535 hospitalized patients aged 79.7 (SD = 6.6) years enrolled at 2 different sites. Each patient was assessed on 2 consecutive days by the research associate who performed the reference delirium assessment. Thereafter, physicians, nurses, and CNAs performed adaptive delirium assessments using the app. Qualitative data to assess the experience of administering the 2-step protocol, and the app usability were also collected and analyzed from 50 physicians, 189 nurses, and 83 CNAs. We used extensible hypertext markup language (XHTML) and JavaScript to develop the app for the iOS-based iPad. The App was linked to Research Electronic Data Capture (REDCap), a relational database system, via a REDCap application programming interface (API) that sent and received data from/to the app. The data from REDCap were sent to the Statistical Analysis System for statistical analysis., Results: The app graphical interface was successfully implemented by XHTML and JavaScript. The API facilitated the instant updating and retrieval of delirium status data between REDCap and the app. Clinicians performed 881 delirium assessments using the app for 535 patients. The transmission of data between the app and the REDCap system showed no errors. Qualitative data indicated that the users were enthusiastic about using the app with no negative comments, 82% positive comments, and 18% suggestions of improvement. Delirium administration time for the 2-step protocol showed similar total time between nurses and physicians (103.9 vs 106.5 seconds). Weekly enrollment reports of the app data were generated for study tracking purposes, and the data are being used for statistical analyses for publications., Discussion: The app developed using iOS could be easily converted to other operating systems such as Android and could be linked to other relational databases beside REDCap, such as electronic health records to facilitate better data retrieval and updating of patient's delirium status., Conclusion: Our app operationalizes an adaptive 2-step delirium screening protocol. Its algorithm and cross-plat formed code of XHTML and JavaScript can be easily exported to other operating systems and hardware platforms, thus enabling wider use of the efficient delirium screening protocol that we have developed. The app is currently implemented as a research tool, but with adaptation could be implemented in the clinical setting to facilitate widespread delirium screening in hospitalized older adults., (© The Author(s) 2021. Published by Oxford University Press on behalf of the American Medical Informatics Association.)

A JavaScript framework named 'jsPsych' developed by de Leeuw (2015) is widely used for conducting Web-based experiments, and its functionality can be enhanced by using plugins. This article introduces a new jsPsych plugin which enables experimenters to set different onset times for geometric figures, images, sounds, and moving objects, and present them synchronized with the refresh of the display. Moreover, this study evaluated the stimulus onset asynchronies (SOAs) using visual and audio stimuli. The results showed that: (i) the deviations from the intended SOAs between two visual stimuli were less than 10 ms, (ii) the variability across browser-computer combinations was reduced compared with the no-plugin condition, and (iii) the variability of the SOAs between visual and audio stimuli was relatively large (about 50 ms). This study concludes that although the use of audio stimuli is somewhat limited, the new plugin provides experimenters with useful and accurate methods for conducting psychophysical experiments online. The latest version of the plugin can be downloaded freely from https://jspsychophysics.hes.kyushu-u.ac.jp under the MIT license.

Web applications can implement procedures for studying the speed of mental processes (mental chronometry) and can be administered via web browsers on most commodity desktops, laptops, smartphones, and tablets. This approach to conducting mental chronometry offers various opportunities, such as increased scale, ease of data collection, and access to specific samples. However, validity and reliability may be threatened by less accurate timing than specialized software and hardware can offer. We examined how accurately web applications time stimuli and register response times (RTs) on commodity touchscreen and keyboard devices running a range of popular web browsers. Additionally, we explored the accuracy of a range of technical innovations for timing stimuli, presenting stimuli, and estimating stimulus duration. The results offer some guidelines as to what methods may be most accurate and what mental chronometry paradigms may suitably be administered via web applications. In controlled circumstances, as can be realized in a lab setting, very accurate stimulus timing and moderately accurate RT measurements could be achieved on both touchscreen and keyboard devices, though RTs were consistently overestimated. In uncontrolled circumstances, such as researchers may encounter online, stimulus presentation may be less accurate, especially when brief durations are requested (of up to 100 ms). Differences in RT overestimation between devices might not substantially affect the reliability with which group differences can be found, but they may affect reliability for individual differences. In the latter case, measurement via absolute RTs can be more affected than measurement via relative RTs (i.e., differences in a participant's RTs between conditions).

AlignmentViewer is a web-based tool to view and analyze multiple sequence alignments of protein families. The particular strengths of AlignmentViewer include flexible visualization at different scales as well as analysis of conservation patterns and of the distribution of proteins in sequence space. The tool is directly accessible in web browsers without the need for software installation. It can handle protein families with tens of thousands of sequences and is particularly suitable for evolutionary coupling analysis, e.g. via EVcouplings.org., Competing Interests: No competing interests were disclosed., (Copyright: © 2020 Reguant R et al.)

AlignmentViewer is a web-based tool to view and analyze multiple sequence alignments of protein families. The particular strengths of AlignmentViewer include flexible visualization at different scales as well as analysis of conservation patterns and of the distribution of proteins in sequence space. The tool is directly accessible in web browsers without the need for software installation. It can handle protein families with tens of thousands of sequences and is particularly suitable for evolutionary coupling analysis, e.g. via EVcouplings.org., Competing Interests: No competing interests were disclosed., (Copyright: © 2020 Reguant R et al.)

Background: As the scope of scientific questions increase and datasets grow larger, the visualization of relevant information correspondingly becomes more difficult and complex. Sharing visualizations amongst collaborators and with the public can be especially onerous, as it is challenging to reconcile software dependencies, data formats, and specific user needs in an easily accessible package., Results: We present substrate, a data-visualization framework designed to simplify communication and code reuse across diverse research teams. Our platform provides a simple, powerful, browser-based interface for scientists to rapidly build effective three-dimensional scenes and visualizations. We aim to reduce the limitations of existing systems, which commonly prescribe a limited set of high-level components, that are rarely optimized for arbitrarily large data visualization or for custom data types., Conclusions: To further engage the broader scientific community and enable seamless integration with existing scientific workflows, we also present pytri, a Python library that bridges the use of substrate with the ubiquitous scientific computing platform, Jupyter. Our intention is to lower the activation energy required to transition between exploratory data analysis, data visualization, and publication-quality interactive scenes., Competing Interests: Competing interests The authors declare that they have no competing interests.

Biological mass spectrometry mainly comprises three fields of endeavor, namely, proteomics, metabolomics, and structural biology. In each of these specialties, the mass spectrometrist needs to access MS 1 mass spectral data, although not necessarily on the same basis. For example, the bottom-up proteomics scientist will occasionally access MS 1 data to perform data inspection, quality assessments, and quantitation measurements, whereas top-down proteomics, structural biology, or metabolomics scientists will actually spend most of their time mining profile-mode MS 1 data. Furthermore, the advent of ion mobility-mass spectrometry imposes new manners of mass spectral data visualization. An open-source MS 1 -only mass data visualization software for the desktop was developed to allow scientists to visualize conventional and drift time mass data. Various mass data integrations are possible, allowing a thorough mass spectral data scrutiny. Isotopic cluster calculations are easily carried over from the chemical formula up to the display of the mass spectrum. Deconvolution of mass peaks can be achieved with a simple mouse drag. Flexible reporting of data inspection events and of mining discoveries is provided. Very large sparse data sets can be sliced into smaller chunks replicating the original data without data loss. Task automation is achieved in a JavaScript environment. This project allows users of mass spectrometry facilities to inspect and mine their MS 1 mass data outside of these facilities without having to resort to the closed-source vendor software shipped with the instruments. mineXpert requires no proprietary software whatsoever once the mass spectrometry data have been converted to mzML. The reference implementation is version 5.8.2 or greater. Reference material, a detailed user manual, and video tutorials are available at http://www.msxpertsuite.org .

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.

The Synthetic Biology Open Language (SBOL) is a data standard for the representation of engineered biological systems. SBOL is implemented in the form of software libraries which can be used to add SBOL support to both new and existing software tools. While existing libraries allow for software to be developed that runs on a server or is installed locally, they lack the capability to create SBOL software that runs directly in a Web browser. Here, we address this issue by presenting sboljs, a JavaScript software library for SBOL that is capable of being used both on the server and in the Web browser.

In this paper, we address an unsolved problem in the real world: how to ensure the integrity of the web content in a browser in the presence of malicious browser extensions? The problem of exposing confidential user credentials to malicious extensions has been widely understood, which has prompted major banks to deploy two-factor authentication. However, the importance of the "integrity" of the web content has received little attention. We implement two attacks on real-world online banking websites and show that ignoring the "integrity" of the web content can fundamentally defeat two-factor solutions. To address this problem, we propose a cryptographic protocol called DOMtegrity to ensure the end-to-end integrity of the DOM structure of a web page from delivering at a web server to the rendering of the page in the user's browser. DOMtegrity is the first solution that protects DOM integrity without modifying the browser architecture or requiring extra hardware. It works by exploiting subtle yet important differences between browser extensions and in-line JavaScript code. We show how DOMtegrity prevents the earlier attacks and a whole range of man-in-the-browser attacks. We conduct extensive experiments on more than 14,000 real-world extensions to evaluate the effectiveness of DOMtegrity., (© The Author(s) 2019.)

Background: Frequent and thorough monitoring of patient safety is a requirement of clinical trials research. Safety data are traditionally reported in a tabular or listing format, which often translates into many pages of static displays. This poses the risk that clinically relevant signals will be obscured by the sheer volume of data reported. Interactive graphics enable the delivery of the vast scope of information found in traditional reports, but allow the user to interact with the charts in real time, focusing on signals of interest., Methods: Clinical research staff, including biostatisticians, project managers, and a medical monitor, were consulted to guide the development of a set of interactive data visualizations that enable key safety assessments for participants. The resulting "Safety Explorer" is a set of 6 interactive, web-based, open source tools designed to address the shortcomings of traditional, static reports for safety monitoring., Results: The Safety Explorer is freely available on GitHub as individual JavaScript libraries: Adverse Event Explorer, Adverse Event Timelines, Safety Histogram, Safety Outlier Explorer, Safety Results Over Time, and Safety Shift Plot; or in a single combined framework: Safety Explorer Suite. The suite can also be utilized through its R interface, the safetyexploreR package., Conclusions: The Safety Explorer provides interactive charts that contain the same information available in standard displays, but the interactive interface allows for improved exploration of patterns and comparisons. Medical Monitors, Safety Review Boards, and Project Teams can use these tools to effectively track and analyze key safety variables and study endpoints.

The Ketcher editor, available as an Open Source software package for drawing chemical structures, has been expanded to include several features that allow storage, management and application of templates, as well as the use of symbols for a planning and processing of solid phase synthesis. In addition, tools for the drawing of coordinative bonds to represent e.g. organometallic compounds were added. The editor has been implemented into an Electronic Lab Notebook (ELN) application which enables the use of the Ketcher editor for advanced operations in chemistry research. The developments of the ELN-integrated Ketcher (ketcher-rails) support the retrieval of identifiers and structure-related information from external databases and the molecule-based calculation of analytical values. The reworked editor can be used to generate molecular structures in reaction templates and to generate syntheses plans.

Background: While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use cases that are not available as features often ends up being difficult. Moreover, existing packages tend to produce standalone widgets that are not designed to serve as middleware, as opposed to flexible tools that can integrate with other components of an application., Results: phylotree.js is a library that extends the popular data visualization framework d3.js, and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees. The effects of such interactions can be captured and communicated to other package components, making it possible to engineer complex and responsive applications that include phylogenetic trees. phylotree.js implements several abstractions in addition to features, and comes with a documented application programming interface, thus promoting interoperability and extensibility. Example applications include a tool to visualize and annotate phylogenetic trees, a web application for comparative sequence analysis, a structural viewer that interacts with a large phylogenetic tree, and an interactive tanglegram., Conclusions: phylotree.js is a useful tool and application module for a variety of computational biology software applications. The code is available on Github and is released under the MIT license.

The evolution of computing and web technologies over the past decade has enabled the development of fully fledged scientific applications that run directly on web browsers. Powered by JavaScript, the lingua franca of web programming, these 'web apps' are starting to revolutionize and democratize scientific research, education, and outreach., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Whenever medical data is integrated from multiple sources, it is regarded good practice to separate data from information about its meaning, such as designations, definitions or permissible values (in short: metadata). However, the ways in which applications work with metadata are imperfect: Many applications do not support fetching metadata from externalized sources such as metadata repositories. In order to display human-readable metadata in any application, we propose not to change the application, but to provide a library that makes a change to the user interface. The goal of this work is to provide a way to "inject" the meaning of metadata keys into the web-based frontend of an application to make it "metadata aware".

Context: Hepatitis C virus (HCV) genotyping at our institution is performed using the Versant HCV genotype 2.0 Line Probe Assay (LiPA). The last steps of this procedure are manual, laborious, and error-prone process that involves the comparison of the banding pattern on a test strip to a physical reference table., Aim: We developed a web-based HCV genotype interpretation platform that utilizes a scanned image to generate the genotypes, thus minimizing interpretation time and reducing error., Subjects and Methods: HCV Genie 2 utilizes a database of banding patterns in conjuncture with image analysis algorithms to determine the genotype for any number of scanned LiPA strips. HCV Genie 2 is built with client-side JavaScript; allowing the program to run in the user' browser rather than on an unknown server, essentially eliminating data and patient privacy concerns., Results: HCV Genie 2 was tested over 2 months and proved identical to human expert interpretation for 148 samples (>1000 bands identified). Manual intervention was required only for two faint bands and one false-positive band; this was done utilizing the built-in-user interface. Utilizing the original method, the trained laboratory technician interpretation time for 16 samples was 13.8 (±0.96) min as compared to 5.0 (±1.09) min with HCV Genie 2, a 63.8% decrease. In addition to the time savings, the new method provides an additional validation step, which decreases the potential for errors., Conclusions: Our institution has moved exclusively to utilize the new techniques and tools described here. Both experienced technicians and the molecular pathologists at our institution prefer the workflow using HCV Genie. It is easier for the technicians to prepare and document, and the pathologists are more rapidly able to review and confirm results. The use of this tool will lead to increase the quality of patient care delivered through this test methodology by decreasing the potential for error. The algorithms developed here can be ported to similar band identification platforms, most directly to other LiPAs., Competing Interests: There are no conflicts of interest.

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.

nodeGame is a free, open-source JavaScript/ HTML5 framework for conducting synchronous experiments online and in the lab directly in the browser window. It is specifically designed to support behavioral research along three dimensions: (i) larger group sizes, (ii) real-time (but also discrete time) experiments, and (iii) batches of simultaneous experiments. nodeGame has a modular source code, and defines an API (application programming interface) through which experimenters can create new strategic environments and configure the platform. With zero-install, nodeGame can run on a great variety of devices, from desktop computers to laptops, smartphones, and tablets. The current version of the software is 3.0, and extensive documentation is available on the wiki pages at http://nodegame.org .

Background: Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge., Results: We developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types. C-State has an interactive, JavaScript-based graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer, pre-processing and prior programming knowledge., Conclusions: C-State is unique in its ability to extract and analyze multi-gene epigenetic information. It allows for powerful GUI-based pattern searching and visualization. We include a case study to demonstrate its potential for identifying user-defined epigenetic trends in context of gene expression profiles.

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., (Copyright © 2017 John Wiley & Sons, Ltd.)

Cheating threatens the validity of unproctored online achievement tests. To address this problem, we developed PageFocus, a JavaScript that detects when participants abandon test pages by switching to another window or browser tab. In a first study, we aimed at testing whether PageFocus could detect and prevent cheating. We asked 115 lab and 186 online participants to complete a knowledge test comprising items that were difficult to answer but easy to look up on the Internet. Half of the participants were invited to look up the solutions, which significantly increased their test scores. The PageFocus script detected test takers who abandoned the test page with very high sensitivity and specificity, and successfully reduced cheating by generating a popup message that asked participants not to cheat. In a second study, 510 online participants completed a knowledge test comprising items that could easily be looked up and a reasoning task involving matrices that were impossible to look up. In a first group, a performance-related monetary reward was promised to the top scorers; in a second group, participants took part in a lottery that provided performance-unrelated rewards; and in a third group, no incentive was offered. PageFocus revealed that participants cheated more when performance-related incentives were offered. As expected, however, this effect was limited to items that could easily be looked up. We recommend that PageFocus be routinely employed to detect and prevent cheating on online achievement tests.

Microsatellites, also known as Simple Sequence Repeats (SSRs), are short tandem repeats of 1-6 nt motifs present in all genomes, particularly eukaryotes. Besides their usefulness as genome markers, SSRs have been shown to perform important regulatory functions, and variations in their length at coding regions are linked to several disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and some may be functional. MSDB (Microsatellite Database) is a collection of >650 million SSRs from 6,893 species including Bacteria, Archaea, Fungi, Plants, and Animals. This database is by far the most exhaustive resource to access and analyze SSR data of multiple species. In addition to exploring data in a customizable tabular format, users can view and compare the data of multiple species simultaneously using our interactive plotting system. MSDB is developed using the Django framework and MySQL. It is freely available at http://tdb.ccmb.res.in/msdb., (© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Background: As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers., (© The Authors 2017. Published by Oxford University Press.)

RNA-Seq Viewer is a web application that enables users to visualize genome-wide expression data from NCBI's Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO) databases. The application prototype was created by a small team during a three-day hackathon facilitated by NCBI at Brandeis University. The backend data pipeline was developed and deployed on a shared AWS EC2 instance. Source code is available at https://github.com/NCBI-Hackathons/rnaseqview., Competing Interests: Competing interests: No competing interests were disclosed.