scholarly journals Web-based metabolic network visualization with a zooming user interface

2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Mario Latendresse ◽  
Peter D Karp
Keyword(s):  
User Interface ◽  
Metabolic Network ◽  
Network Visualization ◽  
Web Based

scholarly journals The BioCyc Metabolic Network Explorer

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Suzanne Paley ◽  
Peter D. Karp
Keyword(s):  
Metabolic Network ◽  
Metabolic Networks ◽  
Dynamic Control ◽  
Software Tool ◽  
Ease Of Use ◽  
Network Visualization ◽  
Software Suite ◽  
Genome Database ◽  
Web Based ◽  
Visualization Tools

Abstract Background The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks. Any metabolic network visualization tool must by necessity show only a subset of all possible metabolite connections, or the results will be visually overwhelming. Existing tools, even those that purport to show an organism’s full metabolic network, limit the set of displayed connections based on predefined pathways or other preselected criteria. We sought instead to provide a tool that would give the user dynamic control over which connections to follow. Results The Metabolic Network Explorer is an easy-to-use, web-based software tool that allows the user to specify a starting metabolite of interest and interactively explore its immediate metabolic neighborhood in either or both directions to any desired depth, letting the user select from the full set of connected reactions. Although, as for other tools, only a small portion of the metabolic network is visible at a time, that portion is selected by the user, based on the full reaction complement, and it is easy to switch among alternate paths of interest. The display is intuitive, customizable, and provides copious links to more detailed information pages. Conclusions The Metabolic Network Explorer fills a gap in the set of metabolic network visualization tools and complements other modes of exploration. Its primary strengths are its ease of use, diagrams that are intuitive to biologists, and its integration with the broader corpus of data provided by a BioCyc Pathway/Genome Database.

Intel® Component Diagnostic Technology: Tools and Education for Intel Component Defect Reduction

2004 ◽  
Author(s):  
Julie S. Doll
Keyword(s):  
User Interface ◽  
Data Management ◽  
Contract Manufacturing ◽  
Defect Reduction ◽  
Web Based ◽  
Technology Tools ◽  
Diagnostic Capability ◽  
Diagnostic Technology

Abstract To enable efficient, accurate debug of Intel architecture components to take place within contract manufacturing sites, and to provide alternatives for the removal of Intel components from, Intel is deploying a diagnostic capability and attendant educational collateral known as to achieve these objectives Intel® Component Diagnostic Technology. This paper will describe details of Intel® Component Diagnostic Technology, including the diagnostic fixture and user interface, diagnostic scripts and analytical coverage, data management and reporting, and on-site and Web-based educational offerings.

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

A framework for programmatically designing user interfaces in JavaScript

2015 ◽  
Vol 11 (3) ◽  
pp. 254-269
Author(s):  
Henry Larkin
Keyword(s):  
User Interface ◽  
User Interfaces ◽  
Design Methodology ◽  
Rapid Development ◽  
Program Code ◽  
Web Based ◽  
Content Type ◽  
Mobile Web ◽  
Mobile Interfaces ◽  
New Framework

Purpose – The purpose of this paper is to investigate the feasibility of creating a declarative user interface language suitable for rapid prototyping of mobile and Web apps. Moreover, this paper presents a new framework for creating responsive user interfaces using JavaScript. Design/methodology/approach – Very little existing research has been done in JavaScript-specific declarative user interface (UI) languages for mobile Web apps. This paper introduces a new framework, along with several case studies that create modern responsive designs programmatically. Findings – The fully implemented prototype verifies the feasibility of a JavaScript-based declarative user interface library. This paper demonstrates that existing solutions are unwieldy and cumbersome to dynamically create and adjust nodes within a visual syntax of program code. Originality/value – This paper presents the Guix.js platform, a declarative UI library for rapid development of Web-based mobile interfaces in JavaScript.

scholarly journals CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalk

2017 ◽  
Author(s):  
Venkata Manem ◽  
George Adam ◽  
Tina Gruosso ◽  
Mathieu Gigoux ◽  
Nicholas Bertos ◽  
...  
Keyword(s):  
Stromal Cells ◽  
Large Scale ◽  
Network Visualization ◽  
Visualization Tool ◽  
Biological Processes ◽  
Web Based ◽  
Link Type ◽  
A Cell ◽  
Large Scale Networks ◽  
User Friendly

ABSTRACTBackground:Over the last several years, we have witnessed the metamorphosis of network biology from being a mere representation of molecular interactions to models enabling inference of complex biological processes. Networks provide promising tools to elucidate intercellular interactions that contribute to the functioning of key biological pathways in a cell. However, the exploration of these large-scale networks remains a challenge due to their high-dimensionality.Results:CrosstalkNet is a user friendly, web-based network visualization tool to retrieve and mine interactions in large-scale bipartite co-expression networks. In this study, we discuss the use of gene co-expression networks to explore the rewiring of interactions between tumor epithelial and stromal cells. We show how CrosstalkNet can be used to efficiently visualize, mine, and interpret large co-expression networks representing the crosstalk occurring between the tumour and its microenvironment.Conclusion:CrosstalkNet serves as a tool to assist biologists and clinicians in exploring complex, large interaction graphs to obtain insights into the biological processes that govern the tumor epithelial-stromal crosstalk. A comprehensive tutorial along with case studies are provided with the application.Availability:The web-based application is available at the following location: http://epistroma.pmgenomics.ca/app/. The code is open-source and freely available from http://github.com/bhklab/EpiStroma-webapp.Contact:[email protected]

scholarly journals An Improved Method for Multi-Lingual News Feed Application

2019 ◽  
Vol 9 (1) ◽  
pp. 6758-6760
Keyword(s):  
User Interface ◽  
Web Application ◽  
New Technologies ◽  
National Language ◽  
The Internet ◽  
Improved Method ◽  
Daily News ◽  
Web Based ◽  
Local Newspaper ◽  
The Web

In the present era, the internet and new technologies are changing the information behavior of news reader .Instead of reading a copy of the local newspaper or watching the scheduledevening news, people increasingly turn to the internet for daily news updates. A Multi-Lingual news feed application is aimed at developing a web based application named multilingual news feed app. This Application deals with the user who wants to read news from the web application. User can select different countries in which a user is interested, the latest news will be fetched from the selected country. The news will be fetched and displayed based on the country selected in its own national language & the news is categorized into 7 different categories. A user can select any category which they are looking for. When you are done selecting the country & category, then the page will automatically refresh and the news will be displayed on MultiLingual news feed application. This application also supports translation and the news can be translated into any language. This application is fully responsive and has a good-looking user interface. The users will find this application much interesting for reading the news articles.

scholarly journals Ugarit: Translation Alignment Visualization

2020 ◽  
Author(s):  
Tariq Yousef
Keyword(s):  
User Interface ◽  
Training Data ◽  
Learning Tool ◽  
Web Based ◽  
Automatic Translation ◽  
Short Overview ◽  
Alignment System ◽  
Visualization Techniques ◽  
Parallel Texts

In this paper we introduce Ugarit a web-based tool for manual translation alignment of parallel texts, the aim was to build a user interface to create training data in form of translation pairs to be used later for an automatic translation alignment system at word/phrase level, the tool now is widely used as reading environment for parallel texts and a languages learning tool. The paper gives a short overview of the visualization techniques used to present the alignment results and shows how the translation graph derived from the aligned translation pairs.

User Interface Adaptation of Web-Based Services on the Semantic Web

2009 ◽  
pp. 711-719 ◽  
Author(s):  
Nikolaos Partarakis ◽  
Constantina Doulgeraki ◽  
Asterios Leonidis ◽  
Margherita Antona ◽  
Constantine Stephanidis
Keyword(s):  
User Interface ◽  
Semantic Web ◽  
Web Based ◽  
Interface Adaptation

Looking for needles in a haystack: how do ebook reader applications handle active indexes? Part 4 - smartphones

2021 ◽  
Vol 39 (1) ◽  
pp. 15-34
Author(s):  
Mary Coe ◽  
Jan Wright
Keyword(s):  
User Interface ◽  
The Other ◽  
Main Concern ◽  
Smartphone Applications ◽  
Tablet Devices ◽  
Web Based ◽  
The Third ◽  
Word Level ◽  
Complex Question

Indexes in ebooks can be ‘active’, with hyperlinks into the text. Should these links go to the page, paragraph, line or word level? This is a complex question, but the main concern may be the user interface in ebook reader applications. In this last article of a four-part series, Mary Coe and Jan Wright report on their investigation of how active ebook indexes are handled by applications on smartphones. They conclude that smartphone applications perform reasonably well but do not handle all levels of locator specificity with precision and that small smartphone screens can lead to problems with index display and use. They also conclude the series with a summary of their findings across all ereading applications and devices. (See also the other articles in this series - the first part on Web-based browser ereader applications in The Indexer 37(2), pp. 125-40; the second part on dedicated ereader devices in The Indexer 38(1), pp. 29-44; and the third part on tablet devices in The Indexer 38(3), pp. 271-89.)

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