Abstract: Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets.

Abstract: We present OpenLambda, a new, open-source platform for building next-generation web services and applications in the burgeoningmodel of serverless computation. We describe the key aspects of serverless computation, and present numerous research challenges that must be addressed in the design and implementation of such systems. We also include a brief study of current web applications, so as to better motivate some aspects of serverless application construction.

Abstract: Worldwide, the number of people and the time spent browsing the web keeps increasing. Accordingly, the technologies to enrich the user experience are evolving at an amazing pace. Many of these evolutions provide for a more interactive web (e.g., boom of JavaScript libraries, weekly innovations in HTML5), a more available web (e.g., explosion of mobile devices), a more secure web (e.g., Flash is disappearing, NPAPI plugins are being deprecated), and a more private web (e.g., increased legislation against cookies, huge success of extensions such as Ghostery and AdBlock). Nevertheless, modern browser technologies, which provide the beauty and power of the web, also provide a darker side, a rich ecosystem of exploitable data that can be used to build unique browser fingerprints. Our work explores the validity of browser fingerprinting in today's environment. Over the past year, we have collected 118,934 fingerprints composed of 17 attributes gathered thanks to the most recent web technologies. We show that innovations in HTML5 provide access to highly discriminating attributes, notably with the use of the Canvas API which relies on multiple layers of the user's system. In addition, we show that browser fingerprinting is as effective on mobile devices as it is on desktops and laptops, albeit for radically different reasons due to their more constrained hardware and software environments. We also evaluate how browser fingerprinting could stop being a threat to user privacy if some technological evolutions continue (e.g., disappearance of plugins) or are embraced by browser vendors (e.g., standard HTTP headers).

Abstract: Solid is a decentralized platform for social Web applications. In the Solid platform, users' data is managed independently of the applications that create and consume this data. Each user stores their data in a Web-accessible personal online datastore (or pod). Each user can have one or more pods from different pod providers, and can easily switch between providers. Applications access data in users' pods using well defined protocols, and a decentralized authentication and access control mechanism guarantees the privacy of the data. In this decentralized architecture, applications can operate on users' data wherever it is stored. Users control access to their data, and have the option to switch between applications at any time. We will demonstrate the utility of Solid and how it is experienced from the point of view of end users and application developers. For this, we will use a set of Solid servers and multiple Web applications that use these servers. We believe that experience with a concrete platform such as Solid is highly valuable in truly appreciating the power of a decentralized social Web.

Abstract: Although Web-based research is now commonplace, it continues to spur skepticism from reviewers and editors, especially whenever reaction times are of primary interest. Such persistent preconceptions are based on arguments referring to increased variation, the limits of certain software and technologies, and a noteworthy lack of comparisons (between Web and lab) in fully randomized experiments. To provide a critical test, participants were randomly assigned to complete a lexical decision task either (a) in the lab using standard experimental software (E-Prime), (b) in the lab using a browser-based version (written in HTML and JavaScript), or (c) via the Web using the same browser-based version. The classical word frequency effect was typical in size and corresponded to a very large effect in all three conditions. There was no indication that the Web- or browser-based data collection was in any way inferior. In fact, if anything, a larger effect was obtained in the browser-based conditions than in the condition relying on standard experimental software. No differences between Web and lab (within the browser-based conditions) could be observed, thus disconfirming any substantial influence of increased technical or situational variation. In summary, the present experiment contradicts the still common preconception that reaction time effects of only a few hundred milliseconds cannot be detected in Web experiments.

Abstract: High-throughput sequencing methods generated allele and single nucleotide polymorphism information for thousands of bacterial strains that are publicly available in online repositories and created the possibility of generating similar information for hundreds to thousands of strains more in a single study. Minimum spanning tree analysis of allelic data offers a scalable and reproducible methodological alternative to traditional phylogenetic inference approaches, useful in epidemiological investigations and population studies of bacterial pathogens. PHYLOViZ Online was developed to allow users to do these analyses without software installation and to enable easy accessing and sharing of data and analyses results from any Internet enabled computer. PHYLOViZ Online also offers a RESTful API for programmatic access to data and algorithms, allowing it to be seamlessly integrated into any third party web service or software. PHYLOViZ Online is freely available at https://online.phyloviz.net.

Abstract: Traffic congestion in metropolitan areas has become more and more serious. Over the past decades, many academic and industrial efforts have been made to alleviate this problem, among which providing accurate, timely and predictive traffic conditions is a promising approach. Nowadays, online open data have rich traffic related information. Typical such resources include official websites of traffic management and operations, web-based map services (like Google map), weather forecasting websites, and local events (sport games, music concerts, etc.) websites. In this paper, online open data are discussed to provide traffic related information. Traffic conditions collected from web based map services are used to demonstrate the feasibility. The stacked long short-term memory model, a kind of deep architecture, is used to learn and predict the patterns of traffic conditions. Experimental results show that the proposed model for traffic condition prediction has superior performance over multilayer perceptron model, decision tree model and support vector machine model.

Abstract: Summary: We here present BioCircos.js, an interactive and lightweight JavaScript library especially for biological data interactive visualization. BioCircos.js facilitates the development of web-based applications for circular visualization of various biological data, such as genomic features, genetic variations, gene expression and biomolecular interactions. Availability and implementation: BioCircos.js and its manual are freely available online at http://bioinfo.ibp.ac.cn/biocircos/. Contact: rschen@ibp.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract: Emerging and re-emerging infectious diseases are a significant public health concern, and early detection and immediate response is crucial for disease control. These challenges have led to the need for new approaches and technologies to reinforce the capacity of traditional surveillance systems for detecting emerging infectious diseases. In the last few years, the availability of novel web-based data sources has contributed substantially to infectious disease surveillance. This study explores the burgeoning field of web-based infectious disease surveillance systems by examining their current status, importance, and potential challenges. A systematic review framework was applied to the search, screening, and analysis of web-based infectious disease surveillance systems. We searched PubMed, Web of Science, and Embase databases to extensively review the English literature published between 2000 and 2015. Eleven surveillance systems were chosen for evaluation according to their high frequency of application. Relevant terms, including newly coined terms, development and classification of the surveillance systems, and various characteristics associated with the systems were studied. Based on a detailed and informative review of the 11 web-based infectious disease surveillance systems, it was evident that these systems exhibited clear strengths, as compared to traditional surveillance systems, but with some limitations yet to be overcome. The major strengths of the newly emerging surveillance systems are that they are intuitive, adaptable, low-cost, and operated in real-time, all of which are necessary features of an effective public health tool. The most apparent potential challenges of the web-based systems are those of inaccurate interpretation and prediction of health status, and privacy issues, based on an individual’s internet activity. Despite being in a nascent stage with further modification needed, web-based surveillance systems have evolved to complement traditional national surveillance systems. This review highlights ways in which the strengths of existing systems can be maintained and weaknesses alleviated to implement optimal web surveillance systems.

Abstract: An area of intensive research under the umbrella of the Internet of Things (IoT) has resulted in intensive proliferation of globally deployed sensor devices that provide a basis for the development of different use-case applications working with real-time data and demanding a rich user interface. Overcoming the lack of the standard HTML platform, HTML5 specifications WebSocket and Canvas graphics strongly supported the development of rich real-time applications. Such support has been offered by browser plug-ins such as Adobe Flash and Microsoft Silverlight for years. In order to provide a deep insight into IoT Web application performance, we implemented two test applications. In the first application, we measured latencies induced by different communication protocols and message encodings, as well as graphics rendering performance, while comparing the performance of different Web platform implementations. In the second application, we compared Web performance of IoT messaging protocols such as MQTT, AMQP, XMPP, and DDS by measuring the latency of sensor data message delivery and the message throughput rate. Our tests have shown that although Adobe Flash has the best performance at the moment, HTML5 platform is also very capable of running real-time IoT Web applications, whereas Microsoft Silverlight is noticeably behind both platforms. On the other hand, MQTT is the most appropriate messaging protocol for a wide set of IoT Web applications. However, IoT application developers should be aware of certain MQTT message broker implementation shortcomings that could prevent the usage of this protocol.

Abstract: In this paper, we introduce a new fine-grained two-factor authentication (2FA) access control system for web-based cloud computing services. Specifically, in our proposed 2FA access control system, an attribute-based access control mechanism is implemented with the necessity of both a user secret key and a lightweight security device. As a user cannot access the system if they do not hold both, the mechanism can enhance the security of the system, especially in those scenarios where many users share the same computer for web-based cloud services. In addition, attribute-based control in the system also enables the cloud server to restrict the access to those users with the same set of attributes while preserving user privacy, i.e., the cloud server only knows that the user fulfills the required predicate, but has no idea on the exact identity of the user. Finally, we also carry out a simulation to demonstrate the practicability of our proposed 2FA system.

Abstract: In this paper, a web-based Internet of things solution aimed for monitoring, tracking and analyzing data in agriculture area is proposed. The purpose of the presented solution is to facilitate monitoring of different manufacturing process in mentioned area using IoT technologies. A real time data is achieved using broker-based publishing/subscribing Message Queue Telemetry Transport protocol which is briefly described. Using this protocol limitations resulting from constrained networks in rural areas are avoided. Collected data from sensors is shown and stored in web part of the information system. An architecture of the web application is described as a client-server three-tier architecture in which the graphical user interface (presentation layer), application functions and logic (application layer) and computer data storage (database layer) are developed and maintained as independent modules, on separate platforms. This type of implementation is developed by the manufacturers need for monitoring and tracking data. This architecture is based on future concrete implementation, at least in segments, in several agricultural facilities in Virovitica-Podravina County.

Abstract: Background: Health information is increasingly presented on the Internet. Several Web design guidelines for older Web users have been proposed; however, these guidelines are often not applied in website development. Furthermore, although we know that older individuals use the Internet to search for health information, we lack knowledge on how they use and evaluate Web-based health information. Objective: This study evaluates user experiences with existing Web-based health information tools among older (≥ 65 years) cancer patients and survivors and their partners. The aim was to gain insight into usability issues and the perceived usefulness of cancer-related Web-based health information tools. Methods: We conducted video-recorded think-aloud observations for 7 Web-based health information tools, specifically 3 websites providing cancer-related information, 3 Web-based question prompt lists (QPLs), and 1 values clarification tool, with colorectal cancer patients or survivors (n=15) and their partners (n=8) (median age: 73; interquartile range 70-79). Participants were asked to think aloud while performing search, evaluation, and application tasks using the Web-based health information tools. Results: Overall, participants perceived Web-based health information tools as highly useful and indicated a willingness to use such tools. However, they experienced problems in terms of usability and perceived usefulness due to difficulties in using navigational elements, shortcomings in the layout, a lack of instructions on how to use the tools, difficulties with comprehensibility, and a large amount of variety in terms of the preferred amount of information. Although participants frequently commented that it was easy for them to find requested information, we observed that the large majority of the participants were not able to find it. Conclusions: Overall, older cancer patients appreciate and are able to use cancer information websites. However, this study shows the importance of maintaining awareness of age-related problems such as cognitive and functional decline and navigation difficulties with this target group in mind. The results of this study can be used to design usable and useful Web-based health information tools for older (cancer) patients.

Abstract: Our study assesses the utility of web-based simulations for developing critical thinking skills and analyzes the relationship between critical thinking and simulation performance. We also explore t...

Abstract: Mobile applications (apps) have long invaded the realm of desktop apps, and hybrid apps become a promising solution for supporting multiple mobile platforms. Providing both platform-specific functionalities via native code like native apps and user interactions via JavaScript code like web apps, hybrid apps help developers build multiple apps for different platforms without much duplicated efforts. However, most hybrid apps are developed in multiple programming languages with different semantics, which may be vulnerable to programmer errors. Moreover, because untrusted JavaScript code may access device-specific features via native code, hybrid apps may be vulnerable to various security attacks. Unfortunately, no existing tools can help hybrid app developers by detecting errors or security holes. In this paper, we present HybriDroid, the first static analysis framework for Android hybrid apps. We investigate the semantics of Android hybrid apps especially for the interoperation mechanism of Android Java and JavaScript. Then, we design and implement a static analysis framework that analyzes inter-communication between Android Java and JavaScript. As example analyses supported by HybriDroid, we implement a bug detector that identifies programmer errors due to the hybrid semantics, and a taint analyzer that finds information leaks cross language boundaries. Our empirical evaluation shows that the tools are practically usable in that they found previously uncovered bugs in real-world Android hybrid apps and possible information leaks via a widely-used advertising platform.

Abstract: Technology advancement induces information technology infusion in business processes and service encounter. The airline industry employs web-based self-service technology (SST), namely, airline online check-in system, to provide more choice, control, and convenience to passengers. Customer adoption intention of web-based SST is particularly momentous, since customer adoption highly drives the service development. Technology acceptance model (TAM), a robust framework measuring factors affecting technology acceptance intention, has been broadly examined in numerous settings. However, inconsistent results are noted in Western and non-Western countries, and the model is challenged from limited cultural orientation. In response to this criticism, this research aims to identify culturally unique dimensions for TAM and construct a framework for hospitality web-based SST adoption from Westerns’ and Asians’ perspectives. Etic–emic approach, incorporating literature search and focus group interviews with Asian resp...

Abstract: Background The B and T lymphocytes are white blood cells playing a key role in the adaptive immunity. A part of their DNA, called the V(D)J recombinations, is specific to each lymphocyte, and enables recognition of specific antigenes. Today, with new sequencing techniques, one can get billions of DNA sequences from these regions. With dedicated Repertoire Sequencing (RepSeq) methods, it is now possible to picture population of lymphocytes, and to monitor more accurately the immune response as well as pathologies such as leukemia. Methods and Results Vidjil is an open-source platform for the interactive analysis of high-throughput sequencing data from lymphocyte recombinations. It contains an algorithm gathering reads into clonotypes according to their V(D)J junctions, a web application made of a sample, experiment and patient database and a visualization for the analysis of clonotypes along the time. Vidjil is implemented in C++, Python and Javascript and licensed under the GPLv3 open-source license. Source code, binaries and a public web server are available at http://www.vidjil.org and at http://bioinfo.lille.inria.fr/vidjil. Using the Vidjil web application consists of four steps: 1. uploading a raw sequence file (typically a FASTQ); 2. running RepSeq analysis software; 3. visualizing the results; 4. annotating the results and saving them for future use. For the end-user, the Vidjil web application needs no specific installation and just requires a connection and a modern web browser. Vidjil is used by labs in hematology or immunology for research and clinical applications.

Abstract: With the development of information technology and popularization of web applications, students nowadays have grown used to skimming through information provided through the Internet. This reading habit led them to be incapable of analyzing or integrating information they have received. Hence, knowledge management and critical thinking (CT) have, in recent years, become important topics in higher education. However, there are many web applications that may serve as effective teaching and learning tools. This study therefore proposed a blended learning environment that incorporated useful web applications within a knowledge transformation model to create an educational environment capable of improving CT and knowledge transformation for student users. A semester-long experiment was then conducted to evaluate this learning environment. Results revealed that the proposed approach was effective in improving student CT and knowledge transformation. Students were also satisfied with the courses and teaching met...

Abstract: Large software organizations such as Facebook or Netflix, who otherwise make daily or even hourly releases of their web applications using continuous delivery, have had to invest heavily into a customized release strategy for their mobile apps, because the vetting process of app stores introduces lag and uncertainty into the release process. Amidst these large, resourceful organizations, it is unknown how the average mobile app developer organizes her app's releases, even though an incorrect strategy might bring a premature app update to the market that drives away customers towards the heavy market competition. To understand the common release strategies used for mobile apps, the rationale behind them and their perceived impact on users, we performed two surveys with users and developers. We found that half of the developers have a clear strategy for their mobile app releases, since especially the more experienced developers believe that it affects user feedback. We also found that users are aware of new app updates, yet only half of the surveyed users enables automatic updating of apps. While the release date and frequency is not a decisive factor to install an app, users prefer to install apps that were updated more recently and less frequently. Our study suggests that an app's release strategy is a factor that affects the ongoing success of mobile apps.

Abstract: JavaScript frameworks, such as jQuery, are widely used for developing web applications. To facilitate using these JavaScript frameworks to implement a feature (e.g., functionality), a large number of programmers often search for code snippets that implement the same or similar feature. However, existing code search approaches tend to be ineffective, without taking into account the fact that JavaScript code snippets often implement a feature based on various relationships (e.g., sequencing, condition, and callback relationships) among the invoked framework API methods. To address this issue, we present a novel Relationship-Aware Code Search (RACS) approach for finding code snippets that use JavaScript frameworks to implement a specific feature. In advance, RACS collects a large number of code snippets that use some JavaScript frameworks, mines API usage patterns from the collected code snippets, and represents the mined patterns with method call relationship (MCR) graphs, which capture framework API methods’ signatures and their relationships. Given a natural language (NL) search query issued by a programmer, RACS conducts NL processing to automatically extract an action relationship (AR) graph, which consists of actions and their relationships inferred from the query. In this way, RACS reduces code search to the problem of graph search: finding similar MCR graphs for a given AR graph. We conduct evaluations against representative real-world jQuery questions posted on Stack Overflow, based on 308,294 code snippets collected from over 81,540 files on the Internet. The evaluation results show the effectiveness of RACS: the top 1 snippet produced by RACS matches the target code snippet for 46% questions, compared to only 4% achieved by a relationship-oblivious approach.

Abstract: Software engineers use record/replay tools to capture use case scenarios that can serve as regression tests for web applications. Such tests, however, can be brittle in the face of code changes. Thus, researchers have sought automated approaches for repairing broken record/replay tests. To date, such approaches have operated by directly analyzing differences between the releases of web applications. Often, however, intermediate versions or commits exist between releases, and these represent finer-grained sequences of changes by which new releases evolve. In this paper, we present WATERFALL, an incremental test repair approach that applies test repair techniques iteratively across a sequence of fine-grained versions of a web application. The results of an empirical study on seven web applications show that our approach is substantially more effective than a coarse-grained approach (209% overall), while maintaining an acceptable level of overhead.

Abstract: The state of web security remains troubling as web applications continue to be favorite targets of hackers. Static analysis tools are important mechanisms for programmers to deal with this problem as they search for vulnerabilities automatically in the application source code, allowing programmers to remove them. However, developing these tools requires explicitly coding knowledge about how to discover each kind of vulnerability. This paper presents a new approach in which static analysis tools learn to detect vulnerabilities automatically using machine learning. The approach uses a sequence model to learn to characterize vulnerabilities based on a set of annotated source code slices. This model takes into consideration the order in which the code elements appear and are executed in the slices. The model created can then be used as a static analysis tool to discover and identify vulnerabilities in source code. The approach was implemented in the DEKANT tool and evaluated experimentally with a set of open source PHP applications and WordPress plugins, finding 16 zero-day vulnerabilities.

Abstract: The large-scale dynamic cloud computing environment has raised great challenges for fault diagnosis in Web applications: First, fluctuating workloads cause traditional application models to change over time; second, modeling the behaviors of complex applications usually requires domain knowledge which is difficult to obtain; third, managing large-scale applications manually is impractical for operators. To address these issues, this paper proposes an automatic fault (F) diagnosis (D) framework for (4) Web applications in cloud (C) computing (FD4C). In this paper, we propose an online incremental clustering method to recognize access behavior patterns. We also use correlation analysis to model the correlations between the workloads and application performance/resource utilization metrics in a specific access behavior pattern. FD4C detects faults by discovering the abrupt changes of correlation coefficients with control charts. Then, FD4C identifies the fault-related metrics using a feature selection method. To evaluate our proposal, we inject typical faults into TPC-W benchmark and apply FD4C to diagnose the injected faults. The experimental results show that FD4C can effectively detect the typical faults and accurately locate the metrics related to the faults.

Abstract: Summary Camera trapping is increasingly becoming an important tool in ecological research. However, the organization of large collections of multimedia files and especially efficient searching for subsets of data is a challenging task. While the development of project-specific software solutions is dominating in the camera trapping community, little attention has been paid to more flexible and open-source solutions supporting diverse camera trapping research projects. We used state of the art and well-recognized open source software components and programming language python to design and implement trapper, a flexible data base driven web application to manage, classify, integrate, share and re-use data in camera trapping projects. The main features of trapper are: (i) it is fully open-source, (ii) it facilitates analysis of videos as well as images, (iii) it provides spatial filtering and web-mapping, (iv) it allows flexible implementation of specific data collection protocols, (v) it is a multi-user and role based system which facilitates collaborative work on camera trapping projects, (vi) it supports data re-use and (re)discovery. trapper can therefore be widely used by ecologists working with a variety of camera trap studies, alone or in collaboration with each other.

Abstract: We present DIME, an integrated solution for the rigorous model-driven development of sophisticated web applications based on the Dynamic Web Application (DyWA) framework, that is designed to accelerate the realization of requirements in agile development environments. DIME provides a family of Graphical Domain-Specific Languages (GDSLs), each of which is tailored towards a specific aspect of typical web applications, including persistent entities (i.e., a data model), business logic in form of various types of process models, the structure of the user interface, and access control. They are modeled on a high level of abstraction in a simplicity-driven fashion that focuses on describing what application is sought, instead of how the application is realized. The choice of platform, programming language, and frameworks is moved to the corresponding (full) code generator.