An On-line MathML Editing Tool for Web Applications

BackgroundMany HIV databases and applications focus on a limited domain of HIV knowledge. Since even a “simple” organism like HIV represents a very complex system with many interacting elements, the fractured structure of existing databases and applications likely limits our ability to investigate and understand HIV. To facilitate research, therefore, we have built HIVToolbox, which integrates much of the knowledge about HIV proteins and presents the data in an interactive web application. HIVToolbox allows quick and convenient hypotheses generation, experiment interpretation, and potential new drug structure creation.MethodsHIVToolbox was built as a standard three-tier J2EE web application, consisting of 1) an underlying relational MySQL database, 2) a set of standard Java data access objects that pull data from the database, and 3) a set of dynamic web pages the user interacts with. HIV-1 data from external sources such as the Protein Data Bank, NCBI, Los Alamos, etc. was collected, curated, and stored in the HIVToolbox database. Additional data, such as homology and position statistics matrices, was generated from existing data. Since version 1, drug binding site and drug resistant mutation data has also been added.ResultsHIVToolbox was used to create several new hypotheses about HIV-1 integrase, including predicting the location of a CK2 phosphorylation site, which was later confirmed by experiment. A new version of HIVToolbox support display of the 3D locations of drug resistant mutations on surface plots of HIV proteins and the drug binding sites for structures of complexes of HIV proteins with drugs.ConclusionHIVToolbox is an open-access web application that allows virologists and structural biologists to access detailed information about HIV-1 proteins, such as sequence, structure, functional sites and relationships, homology, drug binding sites, and drug resistant mutations, and to immediately see the relationships between any or all of them. Weblink: [http://hivtoolbox.bio-toolkit.com]

Management of an inventory data within an agency requires an interactive management system to provide ease and informative data presentation. Data processing using an interactive system makes it easy for users to understand and interact with data, especially if the agency concerned is an agency that is in charge of long-term data storage, complex data processing, data collection and data distribution processes, controlling inventory availability, and data collection conducted every day. Data storage and conventional data processing has several weaknesses such as high error rate in data processing, the system is not interactive so that it troubles and impedes the inventory data collection process by users, and can produce data ambiguity that can cause misinformation. By using the inventory control model Just-In-Time (JIT) Inventory method that allows the compilation of data collection and inventory stock requests as needed so that it can easily distribute and minimize wasted stock, the processing, storage, and data collection of a particular data inventory can be controlled well and can provide clearer information. As a result, implementing inventory control methods into a web application can provide web applications that have better functionality in processing, storing, and collecting data.

Software testing is indispensable to assure software quality. Traditional software testing techniques are insufficient for modern web applications due to their unique characteristics, such as highly dynamic generation of web pages and interactions with DOM elements. Meanwhile, existing web testing techniques are cumbersome to use in long-term maintenance and evolution because the tests are often brittle in the presence of fast changes to web pages. In this paper, we propose an automatic test generation technique for dynamic web applications. Our technique effectively decouples test code from web pages by automatically generating page objects. Based on page objects, our technique performs iterative feedback directed random test generation. Our evaluation on seven real-world web applications demonstrates that the proposed technique achieves reasonable code coverage (from 23.3% to 90.8%) and can effectively explore dynamically generated web pages (around 14.7 times more than the original static web pages), revealing hundreds of HTML issues and five real errors in the applications.

A relevant consequence of the expansion of the web and e-commerce is the growth of the demand of new web sites and web applications. As a result, web sites and applications are usually developed without a formalized process, and web pages are directly coded in an incremental way, where new pages are obtained by duplicating existing ones. Duplicated web pages, having the same structure and just differing for the data they include, can be considered as clones. The identification of clones may reduce the effort devoted to test, maintain and evolve web sites and applications. Moreover, clone detection among different web sites aims to detect cases of possible plagiarism. In this paper we propose an approach. based on similarity metrics, to detect duplicated pages in web sites and applications, implemented with HTML language and ASP technology. The proposed approach has been assessed by analyzing several web sites and Web applications. The obtained results are reported in the paper with respect to some case studies.

It is possible to create interactive, responsive web applications that allow user-generated contributions. However, the relevant technologies have to be explicitly deployed by the authors of the web pages. In this work we present the concept of parasitic and symbiotic web applications which can be deployed on arbitrary web pages by means of a proxy-based application platform. Such applications are capable of inserting, editing and deleting the content of web pages. We use an HTTP proxy in order to insert JavaScript code on each web page that is delivered from the web server to the browser. Additionally we use a database server hosting user-generated scripts as well as high-level APIs allowing for implementing customized web applications. Our approach is capable of cooperating with existing web pages by using shared standards (e.g. formatting of the structure on DOM level) and common APIs but also allows for user-generated (parasitic) applications on arbitrary web pages without the need for cooperation by the page owner.

An unlimited keyboard support is one of the main accessibility requirements for web pages and web applications. But it is not sufficient that the user can perform all actions on the page using the keyboard. In addition designers of web sites or web applications have to make sure that keyboard users can use their pages with acceptable performance. We present GOMS models for mouse and keyboard navigation in web pages and web applications. These models can be used to compare keyboard navigation with mouse navigation. Such a comparison allows us to decide if the amount of keyboard support for a web page or web application is sufficient or if there is an unacceptable disadvantage for keyboard users.

Abstract. With the rapid development in infrastructure, the need to document man-made structures is in increasing demand and inevitable. Such a process of digital documentation of buildings is called Building Information Modelling (BIM). Conventional techniques of BIM involve manual drafting & modelling using computer aided design, drafting & modelling software. Although these techniques are more accurate, given the increase in the size and complexity of modern structures, it would be tedious and time consuming for such manual work. It is in this context LiDAR shows great potential to simplify this task. Laser scanning enables rapid mapping of a building with a high degree of spatial accuracy. Since the spatial point sampling distance of any LiDAR scanner is usually in the order of centimetres or millimetres, this has potential not only to generate high density scans of the building but also to identify even the smallest defects in a structure. This facilitates using LiDAR to study the serviceability of a building. In this project, the feasibility of using a terrestrial laser scanner (TLS) to scan a multi-storey building was investigated. Additionally, the reliability of Potree for visualising point cloud data was tested. Potree is an open-source WebGL based point cloud renderer. Potree enables us to render point clouds and visualise in a portable web application. This application is also capable of making measurements of high accuracy on the 3D model of the library. This could serve to be of great utility in surveying applications. The object of study was chosen as a six-storey building, each floor having differing layouts. Two of these storeys were below ground surface level which also proved to be a test for the reliability of TLS in challenging terrain. The building has a towering height and large footprint which made it a perfect candidate for this project. A total of 54 scans (44 interior scans and 10 exterior scans of the library) were acquired with each subsequent scan station not more than 10m apart from the previous one. This data was brought to the lab for further processing. The processing was carried out using open-source software packages (LAStools, CloudCompare, etc). After processing, the complete point cloud data had 483,292,994 points. In order to make the data easier to handle, spatial sub-sampling of the data was done after which the final point cloud had 87,789,548 points. Finally, this sub-sampled point cloud was published using the open source Potree Converter into an interactive web application.

Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX) to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/

A Curated Web Tracker of Global Development of Treatments and Vaccines for COVID-19

Asynchronous JavaScript and XML (Ajax) is a collection of technologies used to develop rich and interactive Web applications. A typical Ajax client runs locally in the user's Web browser and refreshes its interface on the fly in response to user input. Using this method with the AWS-ECS let us automatically generate test sequences and detect two deviations of their service implementation with respect to the online documentation provided, in less than three minutes of testing. We also provided a framework that allows the runtime monitoring of both client and server contract constraints with minimal modification to an existing Ajax application code. Experiments with the Amazon E-Commerce Service demonstrate the advantages of using a model-based approach for the runtime testing and monitoring of Web applications.

While large-scale low-cost sensor networks are now recording air pollutant concentrations at finer spatial and temporal scales than previously measured, the large environmental data sets generated by these sensor networks can become overwhelming when considering the scientific skills required to analyze the data and generate interpretable results. This paper summarizes the development of an open-source R package (AirSensor) and interactive web application (DataViewer) designed to address the environmental data science challenges of visualizing and understanding local air quality conditions with community networks of low-cost air quality sensors. AirSensor allows users to access historical data, add spatial metadata, and create maps and plots for viewing community monitoring data. The DataViewer application was developed to incorporate the functionality and plotting functions of the R package into a user-friendly web experience that would serve as the primary source for data communication for community-based organizations and citizen scientists.

Recent developments in machine learning have greatly facilitated the design of proteins with improved properties. However, accurately assessing the contributions of an individual or multiple amino acid mutations to overall protein stability to select the most promising mutants remains a challenge. Knowing the specific types of amino acid interactions that improve energetic stability is crucial for finding favorable combinations of mutations and deciding which mutants to test experimentally. In this work, we present an interactive workflow for assessing the energetic contributions of single and multi-mutant designs of proteins. The energy breakdown guided protein design (ENDURE) workflow includes several key algorithms, including per-residue energy analysis and the sum of interaction energies calculations, which are performed using the Rosetta energy function, as well as a residue depth analysis, which enables tracking the energetic contributions of mutations occurring in different spatial layers of the protein structure. ENDURE is available as a web application that integrates easy-to-read summary reports and interactive visualizations of the automated energy calculations and helps users selecting protein mutants for further experimental characterization. We demonstrate the effectiveness of the tool in identifying the mutations in a designed polyethylene terephthalate (PET)-degrading enzyme that add up to an improved thermodynamic stability. We expect that ENDURE can be a valuable resource for researchers and practitioners working in the field of protein design and optimization. ENDURE is freely available for academic use at: http://endure.kuenzelab.org.

Web Applications (WAs) are complex systems and it is difficult to understand their architecture without proper documentation. Due to high pressure of meeting deadlines and short time to market, WAs are liable to be poorly structured and are rarely well documented. Even if documentation is present, it often does not comply with code because code is updated without updating documentation. This leads to problems during maintenance. To improve understanding of a system, attempts can be made to recover architecture from the source code by analyzing the relations and dependencies between a system's components. Architecture of WAs revolves around its web pages (WPs). In this paper, we present a tool for extracting relations between WPs within WAs. WAFE is capable of extracting a large number of relations, and uses combination of procedural language analysis and object oriented language analysis along with WP identifiers (name terms). Another important feature of WAFE tool is its language independence i.e. one can make it functional for any server side language by writing a few regular expressions.

Revisiting the online health information reliability debate in the wake of “web 2.0”: An inter-disciplinary literature and website review

WebWriter: A browser-based editor for constructing Web applications