Single-page Web Application Research Articles

Abstract 5105: A plug-and-play infrastructure for scalable bioinformatics operations

Abstract Genome profiling represents a critical pillar for clinical, translational, and basic research studies. Hospitals, core facilities, and research enterprises invest significant resources to generate genomic data sets. Yet, data management and analysis is frequently manual, which demands significant operator time and often results in siloed resources rendering them as single-use assets. Centralization of the genomic capital in a framework that enables automated processing, metadata integration and continuous interrogation maximizes return for investment and serves as the critical catalyst for research innovation, clinical translation and reproducible research. We developed Isabl, a plug-and-play infrastructure for scalable bioinformatics operations. Isabl provides solutions for databasing, assets management, tracking, automated and reproducible data processing. Dynamic reporting and meta-analysis across data assets is enabled. Isabl is built on four main components. First, an individual-centric and extensible relational database with tracking support for samples (temporal, spatial, aliquot), experimental data (assays, platforms, sequencing runs), cohorts (clinical trials, research projects) and versioned bioinformatics applications (assembly aware, tools, results). Second, the database is exposed through a fully featured RESTful API that enables horizontal integration with information systems such as sequencing cores LIMS, variant visualization platforms like cBioPortal, and where applicable, clinical and biospecimen institutional databases. Third, a Software Development Kit (SDK) built for Next Generation Sequencing assets management. The SDK enables automated execution of data import and language-agnostic bioinformatics applications (alignment, variant calling, post-processing) with support for cohort and individual level reporting features. Furthermore, the SDK facilitates dynamic retrieval of results using vertical and horizontal queries (individual and cohort level, respectively). Lastly, Isabl comes with a Single Page Web Application that fosters user interaction with multidisciplinary teams (i.e. researchers, project coordinators, engineers, clinicians) facilitating tracking of analyses, results visualization, and dynamic query processing. Isabl is currently supporting the Memorial Sloan Kettering Genome Pediatrics Precision Medicine Initiative, a prototype platform that delivers integrated, real-time automated reporting of clinical targeted gene re-sequencing, research whole genome and transcriptome profiling data; as well as linked data from pre-clinical models (i.e. PDX) and single cells studies. As an open-source tool, Isabl democratizes access to a purpose built, automated, scalable and fully integrable bioinformatics architecture. Isabl will be available at https://github.com/isabl-io. Citation Format: Juan S. Medina-Martínez, Juan E. Arango-Ossa, Gunes Gundem, Max F. Levine, Minal Patel, Noushin R. Farnoud, Venkata D. Yellapantula, Gao Teng, Joseph G. Mccarter, Elsa Bernard, Franck Rapaport, Dominik Glodzik, Ross L. Levine, Andrew Kung, Elli Papaemmanuil. A plug-and-play infrastructure for scalable bioinformatics operations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5105.

Cross-modal associations and synesthesia: Categorical perception and structure in vowel\u2013color mappings in a large online sample

We report associations between vowel sounds, graphemes, and colors collected online from over 1,000 Dutch speakers. We also provide open materials, including a Python implementation of the structure measure and code for a single-page web application to run simple cross-modal tasks. We also provide a full dataset of color–vowel associations from 1,164 participants, including over 200 synesthetes identified using consistency measures. Our analysis reveals salient patterns in the cross-modal associations and introduces a novel measure of isomorphism in cross-modal mappings. We found that, while the acoustic features of vowels significantly predict certain mappings (replicating prior work), both vowel phoneme category and grapheme category are even better predictors of color choice. Phoneme category is the best predictor of color choice overall, pointing to the importance of phonological representations in addition to acoustic cues. Generally, high/front vowels are lighter, more green, and more yellow than low/back vowels. Synesthetes respond more strongly on some dimensions, choosing lighter and more yellow colors for high and mid front vowels than do nonsynesthetes. We also present a novel measure of cross-modal mappings adapted from ecology, which uses a simulated distribution of mappings to measure the extent to which participants’ actual mappings are structured isomorphically across modalities. Synesthetes have mappings that tend to be more structured than nonsynesthetes’, and more consistent color choices across trials correlate with higher structure scores. Nevertheless, the large majority (~ 70%) of participants produce structured mappings, indicating that the capacity to make isomorphically structured mappings across distinct modalities is shared to a large extent, even if the exact nature of the mappings varies across individuals. Overall, this novel structure measure suggests a distribution of structured cross-modal association in the population, with synesthetes at one extreme and participants with unstructured associations at the other.

EpiViewer: an epidemiological application for exploring time series data

BackgroundVisualization plays an important role in epidemic time series analysis and forecasting. Viewing time series data plotted on a graph can help researchers identify anomalies and unexpected trends that could be overlooked if the data were reviewed in tabular form; these details can influence a researcher’s recommended course of action or choice of simulation models. However, there are challenges in reviewing data sets from multiple data sources – data can be aggregated in different ways (e.g., incidence vs. cumulative), measure different criteria (e.g., infection counts, hospitalizations, and deaths), or represent different geographical scales (e.g., nation, HHS Regions, or states), which can make a direct comparison between time series difficult. In the face of an emerging epidemic, the ability to visualize time series from various sources and organizations and to reconcile these datasets based on different criteria could be key in developing accurate forecasts and identifying effective interventions. Many tools have been developed for visualizing temporal data; however, none yet supports all the functionality needed for easy collaborative visualization and analysis of epidemic data.ResultsIn this paper, we present EpiViewer, a time series exploration dashboard where users can upload epidemiological time series data from a variety of sources and compare, organize, and track how data evolves as an epidemic progresses. EpiViewer provides an easy-to-use web interface for visualizing temporal datasets either as line charts or bar charts. The application provides enhanced features for visual analysis, such as hierarchical categorization, zooming, and filtering, to enable detailed inspection and comparison of multiple time series on a single canvas. Finally, EpiViewer provides several built-in statistical Epi-features to help users interpret the epidemiological curves.ConclusionEpiViewer is a single page web application that provides a framework for exploring, comparing, and organizing temporal datasets. It offers a variety of features for convenient filtering and analysis of epicurves based on meta-attribute tagging. EpiViewer also provides a platform for sharing data between groups for better comparison and analysis. Our user study demonstrated that EpiViewer is easy to use and fills a particular niche in the toolspace for visualization and exploration of epidemiological data.

AngularJS Performance: A Survey Study

AngularJS is a popular JavaScript MVC-based framework to construct single-page web applications. In this paper, we report the results of a survey with 95 professional developers about performance issues of AngularJS applications. We report common practices followed by developers to avoid performance problems (e.g., use of third-party or custom components), the general causes of performance problems in AngularJS applications (e.g., inadequate architecture decisions taken by AngularJS users), and the technical and specific causes of performance problems (e.g., unnecessary processing included in the digest cycle, which is the internal computation that automatically updates the view with changes detected in the model).

Comparison of front-end frameworks for web applications development

Modern web applications, due to the functionalities they provide in their user interfaces, have a complex program structure. Manually writing a program code, due to the complexity of the entire application, can result in uneven quality and content of individual application parts. Maintaining such developed applications is more difficult. Because of this, web applications are often developed by using different frameworks. A framework allows structuring, simpler and more uniform program script writing, and thus easier web application maintenance. There are various frameworks that can be used in the development of web applications, for different parts of the application. Those analyzed in this paper are used in the development of front end parts of web applications. According to their design, a web application can be developed as the Multi Page (MPA) or the Single Page (SPA). This paper explains the difference between MPA and SPA web applications. The advantages and disadvantages of MPA are demonstrated in relation to SPA web applications. Required characteristics that the framework should have in order to be optimized for creating MPA and SPA web applications are set. The hypothesis has been tested: There is a framework that is optimized for the development of both MPA and SPA applications. Possibilities, architecture and development techniques of a web application using front end frameworks, as well as the suitability of such frameworks for the development of MPA and SPA web applications have been analysed. Choosing a framework for the hypothesis testing has been performed based on the popularity of available frameworks. The required characteristics have been analyzed on the three most popular frameworks: Angular, Vue.js and React-js. It has been shown that the Vue.js framework is the most optimized framework for the development of both MPA and SPA applications.

INCREASE THE SPEED OF WEB APPLICATIONS

The article presents a method of creating a web application based on SPA technology (one-page web application), as a method of increasing the speed of web applications based on the use of modern frameworks, tools and tools for developing client and server part of a one-page web application. One-page web applications are web application technologies that consist of a single web page that interacts with the user, dynamically generating the current page rather than downloading entire new pages from the server. Based on this technique, we developed our own web application and based on it we determined the response rate, which is less than the optimal response rate for single-page web applications. An explanation is given as to which solutions increase response speed and performance in a one-page web application, and why creating a multi-page site is not the best idea. Keywords: single-page web application, database, multi-page web application, non-relational database, relational database, Backend technologies, server, JavaScript

Single Page Application and Canvas Drawing

Recently, with the impact of AJAX a new way of web development techniques have been emerged. Hence, with the help of this model, single-page web application was introduced which can be updated/replaced independently. Today we have a new challenge of building a powerful single-page application using the currently emerged technologies. Gaining an understanding of navigational model and user interface structure of the source application is the first step to successfully build a single- page application. In this paper, it explores not only building powerful single-page application but also Two Dimensional (2D) drawings on images and videos. Moreover, in this research it clearly express the findings on 2D multi-points polygon drawing concepts on client side; real-time data binding in between drawing module on image, video and view pages.

REST 서비스 패턴을 이용한 매시업 클라이언트 뷰 이동 코드 생성

웹 2.0의 확산과 함께 기존의 페이지 간 이동 대신 하나의 페이지에서 여러 개의 웹서비스를 인터페이스하는 웹페이지가 많이 사용되고 있다. 이러한 클라이언트 페이지를 매시업 클라이언트라고 부르는데, 이들은 복잡하고 다양한 기능을 지원하는 제어부를 포함한다. 본 논문에서는 이동 제어의 모델 기반의 코드 생성 방법을 제시한다. 먼저 REST 서비스 패턴을 클라이언트 페이지의 뷰와 뷰 이동에 적용하는 방법을 제안하고, 각 뷰로부터 서비스 메소드 호출이나 뷰 이동이 가능한 타입 조건을 제시한다. 또한 제안된 방법을 적용하여 XForms 페이지의 코드를 자동생성하는 프로토타입 시스템을 개발하였다. 이동 설계 방법을 적용한 매시업 클라이언트 페이지 생성 시스템을 구현하였다. 개발된 자동 생성 시스템은 개발자의 관여 없이 이동 제어 기능을 포함한 클라이언트 페이지의 코드를 생성하며, 체계적인 모델과 이동 패턴에 기반하여 생성된 결과 코드가 이해하기 쉽고 간단하다. 또한 사용자가 필요한 컨트롤만을 포함하여 서비스의 개수가 많아지는 경우에도 적용할 수 있다. As web 2.0 becomes one of the important architecture styles, more web applications adopt single page structure instead of multiple web pages and navigations between pages. A single page web application client, called a mashup client in this paper, interfaces more than one services and allows users to navigate in the page. A mashup client page includes complicated functions and has to handle various styles of services and user requirements, and therefore is usually developed manually. In this paper, we propose a model driven code generation approach for in-page navigations. We propose a page model and view navigation design approach, applying REST service architecture patterns. Then, we consider type conditions for each view to have service calls or navigation controls. Also, we developed an XForms page code generation system to demonstrate the efficiency of the proposed method. The developed system generates mashup client pages including navigation controls between services and views. This system can generate ready to use codes from service specifications, so this can help to reduce the development overhead. Moreover, our approach is based on formal model and navigation patterns so the generated result code is simple and easy to understand, and includes only the necessary controls. Therefore, the proposed approach can be more effective for the case of a large number of services.