Browser Window Research Articles

Declarative layout constraints for testing web applications

The paper focuses on bugs in web applications that can be detected by analyzing the contents and layout of page elements inside a browser's window. Based on an empirical analysis of 35 real-world web sites and applications (such as Facebook, Dropbox, and Moodle), it provides a survey and classification of more than 90 instances of layout-based bugs. It then introduces Cornipickle, an automated testing tool that provides a declarative language to express desirable properties of a web application as a set of human-readable assertions on the page's HTML and CSS data. Such properties can be verified on-the-fly as a user interacts with an application.

A Topographical Approach to Re-Reading Books about Islands in Digital Literary Spaces

This article takes a topographical approach to re-reading print books in digital literary spaces through a discussion of a web-based work of digital literature, …and by islands I mean paragraphs (Carpenter 2013). In this work, a reader is cast adrift in a sea of white space extending far beyond the bounds of the browser window, to the north, south, east and west. This sea is dotted with computer-generated paragraphs. These fluid texts call upon variable strings containing words and phrases collected from a vast literary corpus of books about islands. Individually, each of these textual islands represents a topic—from the Greek topos, meaning place. Collectively they constitute a topographical map of a sustained practice of reading and re-reading and writing and re-writing on the topic of islands. This article argues that, called as statement-events into digital processes, fragments of print texts are reconstituted as events occurring in a digital present which is also a break from the present. A new regime of signification emerges, in which authorship is distributed and text is ‘eventilized’ (Hayles). This regime is situated at the interface between an incoherent aesthetics, one which tends to unravel neat masses, including well-known works of print literature; and an incoherent politics, one which tends to dissolve existing institutional bonds, including bonds of authorship and of place. Galloway terms this regime of signification the ‘dirty regime of truth’.DOI: http://dx.doi.org/10.14195/2182-8830_4-1_5

ASEAN PERSPECTIVES ON THE INTERFACE DESIGN OF LOCATION OF WEB OBJECTS

The majority of web users are constructed with a single standard in mind, or a limited number of user profiles, usually from one country or culture. In order to accommodate the international growth of the Internet, this mono-cultural bias website design must change. If these important steps of a user-centered user-interface (UI) Web Development omitted, the website will be less successful, or may even be dysfunctional. People from different countries and cultures have certain expectations of a particular site that may differ significantly from other countries/ cultures. This study involves the analysis of user perspectives where individuals from different countries and cultures expect a specific web-related object to be located on an interface design. Based on previous studies and is named after its location on the object analysis of user perspectives for the interface design with 94 individuals from 10 ASEAN countries, this paper aims to investigate location of web objects, “Internal links”, “External links”, “Search”, “Login” and “Advertisements”. This study will hope to be able to improve the accuracy of regional perspectives are now recorded. The method of adaptivity from previous studies was used, contains an overview of the browser window, six horizontal and seven vertical grid-based namely, Geometric 42 Grids, on the expected location of the web objects interface design. The goal of the user tests was to examine the perspective of users with different cultural backgrounds. When comparing the final results with previous studies, the following results became clear.

Guide on the Side

Guide on the Side (GotS) is an award-winning application that makes developing interactive, online tutorials simple [1–3]. As the “Guide on the Side” name suggests, each GotS tutorial has an instruction panel—which may contain text, pictures, links, and/or interactive questions—on one side of the browser window and displays the online resource that is the focus of the tutorial on the other side. GotS is open source software that is available without charge from the University of Arizona. Even if you are not sure that your information technology (IT) department will be willing to install GotS, you may want to request a free demo account on the University of Arizona server and give GotS a try [3]. As the Association of College & Research Libraries (ACRL) 2013 Instructional Services Innovation Award committee cochairs have said, the software “allows librarians to easily create tutorials that are both engaging to students and pedagogically sound. GotS serves as a model of the future of library instruction” [1]. The reviewers have been creating online tutorials with GotS in an academic medical library for two years [4]. During that time, we have received many positive comments from students on tutorials created with the product. Students find the navigation tools easy to use, enjoy being able to move through the tutorials at their own pace, and find the interactive questions engaging. One student even described our library’s “PubMed for Clinical Laboratory Science (CLS)” GotS tutorial [5] as, “mind blowingly awesome” and said “[I] never knew how easy searching for research could be.” We used to develop side-guided tutorials using Dreamweaver, but GotS makes this process much easier.

GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.

Motivation: A simple static image of genomes and associated metadata is very limiting, as researchers expect rich, interactive tools similar to the web applications found in the post-Web 2.0 world. GenomeD3Plot is a light weight visualization library written in javascript using the D3 library. GenomeD3Plot provides a rich API to allow the rapid visualization of complex genomic data using a convenient standards based JSON configuration file. When integrated into existing web services GenomeD3Plot allows researchers to interact with data, dynamically alter the view, or even resize or reposition the visualization in their browser window. In addition GenomeD3Plot has built in functionality to export any resulting genome visualization in PNG or SVG format for easy inclusion in manuscripts or presentations.Results: GenomeD3Plot is being utilized in the recently released Islandviewer 3 (www.pathogenomics.sfu.ca/islandviewer/) to visualize predicted genomic islands with other genome annotation data. However, its features enable it to be more widely applicable for dynamic visualization of genomic data in general.Availability and implementation: GenomeD3Plot is licensed under the GNU-GPL v3 at https://github.com/brinkmanlab/GenomeD3Plot/.Contact: brinkman@sfu.ca

JsNMR: an embedded platform-independent NMR spectrum viewer.

jsNMR is a lightweight NMR spectrum viewer written in JavaScript/HyperText Markup Language (HTML), which provides a cross-platform spectrum visualizer that runs on all computer architectures including mobile devices. Experimental (and simulated) datasets are easily opened in jsNMR by (i) drag and drop on a jsNMR browser window, (ii) by preparing a jsNMR file from the jsNMR web site, or (iii) by mailing the raw data to the jsNMR web portal. jsNMR embeds the original data in the HTML file, so a jsNMR file is a self-transforming dataset that may be exported to various formats, e.g. comma-separated values. The main applications of jsNMR are to provide easy access to NMR data without the need for dedicated software installed and to provide the possibility to visualize NMR spectra on web sites.

SENTINEL: Securing Legacy Firefox Extensions

A poorly designed web browser extension with a security vulnerability may expose the whole system to an attacker. Therefore, attacks directed at “benign-but-buggy” extensions, as well as extensions that have been written with malicious intent, pose significant security threats to a system running such components. Recent studies have indeed shown that many Firefox extensions are over-privileged, making them attractive attack targets. Unfortunately, users currently do not have many options when it comes to protecting themselves from extensions that may potentially be malicious. Once installed and executed, the extension is considered trusted.This paper introduces SENTINEL, a policy enforcer for the Firefox browser that gives fine-grained control to the user over the actions of existing JavaScript Firefox extensions. The user is able to define policies (or use predefined ones) and block common attacks such as data exfiltration, remote code execution, saved password theft, preference modification, phishing, browser window clickjacking, and namespace collision exploits. Our evaluation of SENTINEL shows that our prototype implementation can effectively prevent concrete, real-world Firefox extension attacks without a detrimental impact on the user's browsing experience.

Homenet3D: a new view on home network state

Although it performs an increasingly important role in our lives, the home network remains a bit of a mystery when end users wish to know what is “happening on the inside.” This article introduces Homenet3D, an open source project that allows users to view their home network's state as objects in 3D space within a web browser window. Homenet3D maps quantitative state to the shape, size, spin, bounce, and/or color of selected objects to qualitatively communicate what is happening on the network. We describe our Homenet3D implementation for routers running OpenWRT, and discuss the potential for visualizing multirouter/ multi-subnet home networks.

MeT-DB: a database of transcriptome methylation in mammalian cells.

Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. The MethylTranscriptome DataBase (MeT-DB, http://compgenomics.utsa.edu/methylation/) is the first comprehensive resource for N6-methyladenosine (m6A) in mammalian transcriptome. It includes a database that records publicaly available data sets from methylated RNA immunoprecipitation sequencing (MeRIP-Seq), a recently developed technology for interrogating m6A methyltranscriptome. MeT-DB includes ∼300k m6A methylation sites in 74 MeRIP-Seq samples from 22 different experimental conditions predicted by exomePeak and MACS2 algorithms. To explore this rich information, MeT-DB also provides a genome browser to query and visualize context-specific m6A methylation under different conditions. MeT-DB also includes the binding site data of microRNA, splicing factor and RNA binding proteins in the browser window for comparison with m6A sites and for exploring the potential functions of m6A. Analysis of differential m6A methylation and the related differential gene expression under two conditions is also available in the browser. A global perspective of the genome-wide distribution of m6A methylation in all the data is provided in circular ideograms, which also act as a navigation portal. The query results and the entire data set can be exported to assist publication and additional analysis.

Online access to the Kalgutkar and Jansonius database of fossil fungi

An important compendium of fossil fungi is now publicly available through a searchable online database. The original compendium was the work of Kalgutkar and Jansonius, who combed through 238 references and collated and annotated published descriptions for 1783 taxa of fungal fossils. By translating these data to a FileMaker Pro database and to the Web, we increase options for searching, sorting, annotating and updating this information. Database search results provide lists of names, ages and thumbnail images of palynomorphs. An individual record from the results list can be expanded in a new browser window to show a complete description for a taxon. The database is timely because developments in molecular systematics are helping to place spore characters in a phylogenetic framework. Some of the previously ambiguous fossil fungi can now be placed into phylogenetic lineages. We anticipate that the Web version of the data will serve as a convenient entry point into the fungal fossil record, leading to integration of more information from fossils into fungal phylogenies.

Eight short talks about islands … and by islands I mean paragraphs

Abstract Flocks of books open and close, winging their way web-ward. A reader is cast adrift in a sea of white space veined blue by lines of longitude, of latitude, of graph, of paper. The horizon extends far beyond the bounds of the browser window, to the north, south, east and west. Navigating this space (with track pad, touch screen, mouse or arrow keys) reveals that this sea is dotted with islands… and by islands I mean paragraphs. These fluid texts are continuously recomposed by JavaScript files calling upon variable strings containing words and phrases collected from a vast literary corpus – Deleuze’s Desert Islands (2004), Shakespeare’s The Tempest (1610–11), Defoe’s Robinson Crusoe (1719), Bishop’s Crusoe in England (1971), Coetzee’s Foe (1966), Ballard’s Concrete Island (1973), Hakluyt’s Voyages and Discoveries (1598–1600), Darwin’s Voyages of the Beagle (1838), and many other lesser-known sources including an out-of-date guidebook to the Scottish Isles, and an amalgam of accounts of the classical and quite possibly fictional island of Thule. Individually, each of these textual islands represents a topic – from the Greek topos, meaning place. Collectively they constitute a topographical map of a sustained practice of reading and re-reading and writing and re-writing on the topic of islands. In this constantly shifting sea of variable texts a reader will never wash ashore on the same island twice… and by islands, I really do mean paragraphs.

Online Persona as Hybrid-Object: Tracing the Problems and Possibilities of Persona in the Short Film Noah

Online Persona as Hybrid-Object: Tracing the Problems and Possibilities of Persona in the Short Film Noah

Logout in single sign-on systems: Problems and solutions

Web single sign-on (SSO) systems enable users to authenticate themselves to multiple online services with one authentication credential and mechanism offered by an identity provider. The topic is widely studied and many solutions exist. However, logging out of a service using SSO has received less attention. While previous studies note that users want single logout when using SSO, most of the existing services do not offer it, and the identity providers do not even keep track of the open sessions. This article describes challenges related to logout in federated identity management and analyzes unexpected behavior in logout situations. The examples are from the Shibboleth SSO system. Based on the analysis, we give guidelines for implementing reliable logout and describe a polling-based solution for creating a system-wide logout mechanisms that only requires minor changes to the existing code and does not burden the identity provider excessively. In addition to the system-wide logout, our solution gives users the option to log out of only one service. A usability test was conducted to evaluate the solution. The results show that the users liked the ability to choose between the two logout options, but they did not understand the words used to describe them. Another observation was that a majority of the users do not log out of the services at all; they just close the browser window, which should be taken into account in the design of web SSO systems.

Online repository of three-dimensional models of brain structures

Event Abstract Back to Event Online repository of three-dimensional models of brain structures Piotr Majka1*, Jakub M. Kowalski1, Natalia Chlodzinska1 and Daniel K. Wójcik1 1 Nencki Institute of Experimental Biology, Poland Brain atlases provide key reference frameworks for neuroscience. With the advancement of technology traditional 2D atlases are being complemented by digital 3D atlases, which are more flexible and better adapted to address modern computational, analytical and visualisation challenges of neuroscience. Although the number of available brain atlases grows, the set of tools facilitating systematic access to these data is limited. To provide an easy access to a range of neuroanatomical data we created the 3D Brain Atlas Reconstructor web service ( http://service.3dbar.org ) – an on-line repository of brain atlases and 3D models of brain structures. The essential part of the 3dBAR service is a browser-based interface providing a wide range of functionalities including: - Browsing and downloading of reconstructed 3D models of brain structures in form of polygonal mesh or a volumetric dataset; - Previewing and manipulating the models within the browser window using WebGL technology, without necessity of installing additional software; - Accessing and downloading brain atlas packages consisting of a series of SVG slices or labelled NIfTI volumes; - Generation and management of custom reconstructions (e.g. processed with non-standard pipeline or generating result in an additional file format) using on-line reconstruction wizard. Currently, there are several atlases available through the service, including various delineations of the INCF Waxholm Space mouse brain reference, Allen Brain Institute mouse reference atlas, and a collection of atlases distributed by the Scalable Brain Atlas project ( http://scalablebrainatlas.incf.org ). Some of them are intrinsically 3D atlases based on MRI scans while others are reconstructed from collections of 2D delineations. We can also host additional atlases. Modern data repository should provide a convenient interface for data exchange and allow integration of its services with other systems or software. To facilitate interoperability with third-party applications we offer a complete application programming interface consisting of a set of HTTP queries providing the developers with programmatic access to resources we provide. Currently this mechanism is used by ScalableBrainAtlas, Neurolex.org website and WaxML services developed by INCF DAI. The project is supported by an infrastructural grant from the Polish Ministry of Regional Development POIG.02.03.00-00-003/09. Keywords: digital atlasing, 3D models, computational neuroscience, Brain Atlas, web services Conference: 5th INCF Congress of Neuroinformatics, Munich, Germany, 10 Sep - 12 Sep, 2012. Presentation Type: Poster Topic: Neuroinformatics Citation: Majka P, Kowalski J, Chlodzinska N and Wójcik D (2014). Online repository of three-dimensional models of brain structures. Front. Neuroinform. Conference Abstract: 5th INCF Congress of Neuroinformatics. doi: 10.3389/conf.fninf.2014.08.00107 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 21 Mar 2013; Published Online: 27 Feb 2014. * Correspondence: Dr. Piotr Majka, Nencki Institute of Experimental Biology, Warsaw, Poland, p.majka@nencki.edu.pl Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Piotr Majka Jakub M. Kowalski Natalia Chlodzinska Daniel K. Wójcik Google Piotr Majka Jakub M. Kowalski Natalia Chlodzinska Daniel K. Wójcik Google Scholar Piotr Majka Jakub M. Kowalski Natalia Chlodzinska Daniel K. Wójcik PubMed Piotr Majka Jakub M. Kowalski Natalia Chlodzinska Daniel K. Wójcik Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Dynamic Interactive Educational Diabetes Simulations Using the World Wide Web: An Experience of More Than 15 Years with AIDA Online

Background. AIDA is a widely available downloadable educational simulator of glucose-insulin interaction in diabetes. Methods. A web-based version of AIDA was developed that utilises a server-based architecture with HTML FORM commands to submit numerical data from a web-browser client to a remote web server. AIDA online, located on a remote server, passes the received data through Perl scripts which interactively produce 24 hr insulin and glucose simulations. Results. AIDA online allows users to modify the insulin regimen and diet of 40 different prestored “virtual diabetic patients” on the internet or create new “patients” with user-generated regimens. Multiple simulations can be run, with graphical results viewed via a standard web-browser window. To date, over 637,500 diabetes simulations have been run at AIDA online, from all over the world. Conclusions. AIDA online's functionality is similar to the downloadable AIDA program, but the mode of implementation and usage is different. An advantage to utilising a server-based application is the flexibility that can be offered. New modules can be added quickly to the online simulator. This has facilitated the development of refinements to AIDA online, which have instantaneously become available around the world, with no further local downloads or installations being required.

3D Digitisation and Visualisation of the Vače Situla

EXTENDED ABSTRACT:The project of 3D digitisation and visualisation of the Vače situla was implemented at the beginning of 2011 in cooperation with the National Museum of Slovenia where the situla is kept and the company MFC.2 which, among other services, develops and implements 3 D digitisation and visualisation projects. The purpose of the project was to digitise and visualise a famous and precious piece of cultural heritage and to 1. show what modern 3D shape and texture scanning technologies allow us to do, 2. show how to ensure safety and reach high quality in digitising cultural heritage objects. 3. measure the added value of the 3 D visualisation of cultural heritage as a powerful tool for preservation, conservation, research, education, knowledge sharing and promotion of cultural heritage objects. Furthermore, the aims of the project were: 1. 3D capture of the shape and texture of the situla using the 3D scanning method. 2. 3D image of the situla and its details with expert descriptions. 3. 3D stereoscopic projection of the situla viewed with 3D glasses and with the possibility of controlling it remotely. 4. 3D animation giving professional interpretation of certain facts about the situla. 5. Public presentation of the project results on Slovenian cultural holiday, 8th February 2011, at the National Museum of Slovenia. The 3D capture of the shape and texture of the situla was carried out using the white light 3D scanning method followed by 3D flesh animation to show the object and its details. A touch screen was used to provide user access to the content. Reality based model enabled vertical rotation of the situla as well as the interactive display of individual engravings. By clicking a situla detail a photo with an extensive professional explanation of the scene was displayed in a new browser window. For attractive public presentation of the exhibition a 3D stereoscopic animation of the situla rotating and seemingly floating in the atrium of the National Museum of Slovenia was displayed. Visitors had the possibility to view the animation with 3D glasses and to navigate the floating situla remotely. Furthermore, a 3D animation of the situla history was created and entitled the Story of the Vače Situla. Based on expert interpretation it presented the origins of the situla, the period in which it was produced, the geographic area where its production was spread, usability of situlas and its discovery in Vače at the end of 19th century. The animation includes text, sound and picture presentation of the situla and is enriched by animation of one of small figures depicting everyday life and tasks among the people. The aims of the project were presented to public on Slovenian cultural holiday, 8th February 2011, in the atrium of the national Museum at Prešernova in Ljubljana at a cultural event entitled the Third Dimension of the Vače Situla. The visitors had the opportunity to test the new technology of remote control of 3D objects as well as 3D scanning and capturing the shape and texture of material objects. The public response was very favourable indicating the importance of modern technological approaches in presenting our cultural heritage. The value of 3D technologies in capturing and visualisation of cultural heritage was proved: 1. They enable multiuser and interactive access to 3D content. 2. 3D metadata serve for educational purposes, public presentations, exhibitions and promotion of cultural heritage, 3. They offer new opportunities to spread information on cultural heritage objects. 4. Virtual objects are presented in a user friendly, intuitive and attractive way.

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era

The Eukaryotic Promoter Database (EPD), available online at http://epd.vital-it.ch, is a collection of experimentally defined eukaryotic POL II promoters which has been maintained for more than 25 years. A promoter is represented by a single position in the genome, typically the major transcription start site (TSS). EPD primarily serves biologists interested in analysing the motif content, chromatin structure or DNA methylation status of co-regulated promoter subsets. Initially, promoter evidence came from TSS mapping experiments targeted at single genes and published in journal articles. Today, the TSS positions provided by EPD are inferred from next-generation sequencing data distributed in electronic form. Traditionally, EPD has been a high-quality database with low coverage. The focus of recent efforts has been to reach complete gene coverage for important model organisms. To this end, we introduced a new section called EPDnew, which is automatically assembled from multiple, carefully selected input datasets. As another novelty, we started to use chromatin signatures in addition to mRNA 5′tags to locate promoters of weekly expressed genes. Regarding user interfaces, we introduced a new promoter viewer which enables users to explore promoter-defining experimental evidence in a UCSC genome browser window.

Output Keywords in Context in an HTML File with Python

This lesson builds on 'Keywords in Context (Using N-grams)', where n-grams were extracted from a text. Here, you will learn how to output all of the n-grams of a given keyword in a document downloaded from the Internet, and display them clearly in your browser window.

Arachne—A web-based event viewer for [formula omitted

Neutrino interaction events in the MINERνA detector are visually represented with a web-based tool called Arachne. Data are retrieved from a central server via AJAX, and client-side JavaScript draws images into the user's browser window using the draft HTML 5 standard. These technologies allow neutrino interactions to be viewed by anyone with a web browser, allowing for easy hand-scanning of particle interactions. Arachne has been used in MINERνA to evaluate neutrino data in a prototype detector, to tune reconstruction algorithms, and for public outreach and education.

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

SCOPE is an ensemble motif finder that uses three component algorithms in parallel to identify potential regulatory motifs by over-representation and motif position preference1. Each component algorithm is optimized to find a different kind of motif. By taking the best of these three approaches, SCOPE performs better than any single algorithm, even in the presence of noisy data1. In this article, we utilize a web version of SCOPE2 to examine genes that are involved in telomere maintenance. SCOPE has been incorporated into at least two other motif finding programs3,4 and has been used in other studies5-8. The three algorithms that comprise SCOPE are BEAM9, which finds non-degenerate motifs (ACCGGT), PRISM10, which finds degenerate motifs (ASCGWT), and SPACER11, which finds longer bipartite motifs (ACCnnnnnnnnGGT). These three algorithms have been optimized to find their corresponding type of motif. Together, they allow SCOPE to perform extremely well. Once a gene set has been analyzed and candidate motifs identified, SCOPE can look for other genes that contain the motif which, when added to the original set, will improve the motif score. This can occur through over-representation or motif position preference. Working with partial gene sets that have biologically verified transcription factor binding sites, SCOPE was able to identify most of the rest of the genes also regulated by the given transcription factor. Output from SCOPE shows candidate motifs, their significance, and other information both as a table and as a graphical motif map. FAQs and video tutorials are available at the SCOPE web site which also includes a "Sample Search" button that allows the user to perform a trial run. Scope has a very friendly user interface that enables novice users to access the algorithm's full power without having to become an expert in the bioinformatics of motif finding. As input, SCOPE can take a list of genes, or FASTA sequences. These can be entered in browser text fields, or read from a file. The output from SCOPE contains a list of all identified motifs with their scores, number of occurrences, fraction of genes containing the motif, and the algorithm used to identify the motif. For each motif, result details include a consensus representation of the motif, a sequence logo, a position weight matrix, and a list of instances for every motif occurrence (with exact positions and "strand" indicated). Results are returned in a browser window and also optionally by email. Previous papers describe the SCOPE algorithms in detail1,2,9-11.