scholarly journals WHONDRS-GUI: a web application for global survey of surface water metabolites

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9277
Author(s):  
Xinming Lin ◽  
Huiying Ren ◽  
Amy E. Goldman ◽  
James C. Stegen ◽  
Timothy D. Scheibe
Keyword(s):  
User Interface ◽  
Surface Water ◽  
Web Application ◽  
Data Types ◽  
Global Survey ◽  
Link Type ◽  
Sampling Campaign ◽  
Domain Integration ◽  
River Corridors ◽  
The Web

Background The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL). The obtained knowledge and data package inform mechanistic and data-driven models to enhance predictions of outcomes of hydrologic perturbations and watershed function, one of the most critical components in model-data integration. To support efforts of the multi-domain integration and make the ever-growing data package more accessible for researchers across the world, a Shiny/R Graphical User Interface (GUI) called WHONDRS-GUI was created. Results The web application can be run on any modern web browser without any programming or operational system requirements, thus providing an open, well-structured, discoverable dataset for WHONDRS. Together with a context-aware dynamic user interface, the WHONDRS-GUI has functionality for searching, compiling, integrating, visualizing and exporting different data types that can easily be used by the community. The web application and data package are available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1484811, which enables users to simultaneously obtain access to the data and code and to subsequently run the web app locally. The WHONDRS-GUI is also available for online use at Shiny Server (https://xmlin.shinyapps.io/whondrs/).

scholarly journals LandScape: a web application for interactive genomic summary visualization

2019 ◽  
Author(s):  
Wenlong Jia ◽  
Hechen Li ◽  
Shiying Li ◽  
Shuaicheng Li
Keyword(s):  
Genetic Information ◽  
Web Application ◽  
Genomic Research ◽  
File Format ◽  
Data Types ◽  
Web Based ◽  
Link Type ◽  
Level Data ◽  
Real Time Visualization ◽  
Information Landscape

ABSTRACTSummaryVisualizing integrated-level data from genomic research remains a challenge, as it requires sufficient coding skills and experience. Here, we present LandScapeoviz, a web-based application for interactive and real-time visualization of summarized genetic information. LandScape utilizes a well-designed file format that is capable of handling various data types, and offers a series of built-in functions to customize the appearance, explore results, and export high-quality diagrams that are available for publication.Availability and implementationLandScape is deployed at bio.oviz.org/demo-project/analyses/landscape for online use. Documentation and demo data are freely available on this website and GitHub (github.com/Nobel-Justin/Oviz-Bio-demo)[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 re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11333
Author(s):  
Daniyar Karabayev ◽  
Askhat Molkenov ◽  
Kaiyrgali Yerulanuly ◽  
Ilyas Kabimoldayev ◽  
Asset Daniyarov ◽  
...  
Keyword(s):  
Web Application ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
Data Types ◽  
Standard Format ◽  
Standard Data ◽  
Additional Information ◽  
Link Type ◽  
Sequencing Platforms ◽  
User Friendly

Background High-throughput sequencing platforms generate a massive amount of high-dimensional genomic datasets that are available for analysis. Modern and user-friendly bioinformatics tools for analysis and interpretation of genomics data becomes essential during the analysis of sequencing data. Different standard data types and file formats have been developed to store and analyze sequence and genomics data. Variant Call Format (VCF) is the most widespread genomics file type and standard format containing genomic information and variants of sequenced samples. Results Existing tools for processing VCF files don’t usually have an intuitive graphical interface, but instead have just a command-line interface that may be challenging to use for the broader biomedical community interested in genomics data analysis. re-Searcher solves this problem by pre-processing VCF files by chunks to not load RAM of computer. The tool can be used as standalone user-friendly multiplatform GUI application as well as web application (https://nla-lbsb.nu.edu.kz). The software including source code as well as tested VCF files and additional information are publicly available on the GitHub repository (https://github.com/LabBandSB/re-Searcher).

scholarly journals Knowledge.Bio: A Web Application for Exploring, Building and Sharing Webs of Biomedical Relationships Mined from PubMed

2016 ◽  
Author(s):  
Richard Bruskiewich ◽  
Kenneth Huellas-Bruskiewicz ◽  
Farzin Ahmed ◽  
Rajaram Kaliyaperumal ◽  
Mark Thompson ◽  
...  
Keyword(s):  
User Interface ◽  
Text Mining ◽  
Graphical User Interface ◽  
Biomedical Research ◽  
Web Application ◽  
Source Code ◽  
Research Literature ◽  
Knowledge Networks ◽  
Link Type ◽  
Web Platform

AbstractKnowledge.Bio is a web platform that enhances access and interpretation of knowledge networks extracted from biomedical research literature. The interaction is mediated through a collaborative graphical user interface for building and evaluating maps of concepts and their relationships, alongside associated evidence. In the first release of this platform, conceptual relations are drawn from the Semantic Medline Database and the Implicitome, two compleme ntary resources derived from text mining of PubMed abstracts.Availability— Knowledge.Bio is hosted at http://knowledge.bio/ and the open source code is available at http://bitbucket.org/sulab/kb1/.Contact— [email protected]; [email protected]

scholarly journals HTTP-Request Classification in Automatic Web Application Crawling

2021 ◽  
Vol 33 (3) ◽  
pp. 77-86
Author(s):  
Anna Vadimovna Lapkina ◽  
Andrew Alexandrovitch Petukhov
Keyword(s):  
User Interface ◽  
Web Application ◽  
Complete Information ◽  
Interface Elements ◽  
Server Side ◽  
Interaction Interaction ◽  
Client Request ◽  
Developer Tools ◽  
Using Data ◽  
The Web

The problem of automatic requests classification, as well as the problem of determining the routing rules for the requests on the server side, is directly connected with analysis of the user interface of dynamic web pages. This problem can be solved at the browser level, since it contains complete information about possible requests arising from interaction interaction between the user and the web application. In this paper, in order to extract the classification features, using data from the request execution context in the web client is suggested. A request context or a request trace is a collection of additional identification data that can be obtained by observing the web page JavaScript code execution or the user interface elements changes as a result of the interface elements activation. Such data, for example, include the position and the style of the element that caused the client request, the JavaScript function call stack, and the changes in the page's DOM tree after the request was initialized. In this study the implementation of the Chrome Developer Tools Protocol is used to solve the problem at the browser level and to automate the request trace selection.

scholarly journals CLINE: a web-tool for the comparison of biological dendrogram structures

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Rodolfo S. Allendes Osorio ◽  
Lokesh P. Tripathi ◽  
Kenji Mizuguchi
Keyword(s):  
User Interface ◽  
Open Access ◽  
Special Interest ◽  
Web Application ◽  
Source Code ◽  
Visualization Tool ◽  
Web Tool ◽  
Link Type ◽  
Multiple Structures ◽  
Biological Interpretation

Abstract Background When visually comparing the results of hierarchical clustering, the differences in the arrangements of components are of special interest. However, in a biological setting, identifying such differences becomes less straightforward, as the changes in the dendrogram structure caused by permuting biological replicates, do not necessarily imply a different biological interpretation. Here, we introduce a visualization tool to help identify biologically similar topologies across different clustering results, even in the presence of replicates. Results Here we introduce CLINE, an open-access web application that allows users to visualize and compare multiple dendrogram structures, by visually displaying the links between areas of similarity across multiple structures. Through the use of a single page and a simple user interface, the user is able to load and remove structures form the visualization, change some aspects of their display and set the parameters used to match cluster topology across consecutive pairs of dendrograms. Conclusions We have implemented a web-tool that allows the users to visualize different dendrogram structures, showing not only the structures themselves, but also linking areas of similarity across multiple structures. The software is freely available at http://mizuguchilab.org/tools/cline/. Also, the source code, documentation and installation instructions are available on GitHub at https://github.com/RodolfoAllendes/cline/.

scholarly journals Text and Voice Based Emotion Monitoring System

2020 ◽  
Vol 12 (4) ◽  
pp. 194-200
Author(s):  
Anil S Naik
Keyword(s):  
User Interface ◽  
Monitoring System ◽  
Call Center ◽  
Web Application ◽  
Android Application ◽  
Emotion Detection ◽  
Report Generation ◽  
Emotion Analysis ◽  
Model View ◽  
The Web

An Emotion monitoring system for a call-center is proposed. It aims to simplify the tracking and management of emotions extracted from call center Employee-Customer conversations. The system is composed of four modules: Emotion Detection, Emotion Analysis and Report Generation, Database Manager, and User Interface. The Emotion Detection module uses Tone Analyzer to extract them for reliable emotion; it also performs the Utterance Analysis for detecting emotion. The 14 emotions detected by the tone analyzer are happy, joy, anger, sad and neutral, etc. The Emotion Analysis module performs classification into the 3 categories: Neutral, Anger and Joy. By using this category, it applies the point-scoring technique for calculating the Employee Score. This module also polishes the output of the Emotion Detection module to provide a more presentable output of a sequence of emotions of the Employee and the Customer. The Database Manager is responsible for the management of the database wherein it handles the creation, and update of data. The Interface module serves as the view and user interface for the whole system. The system is comprised of an Android application for conversation and a web application to view reports. The Android application was developed using Android Studio to maintain the modularity and flexibility of the system. The local server monitors the conversation, it displays the detected emotions of both the Customer and the Employee. On the other hand, the web application was constructed using the Django Framework to maintain its modularity and abstraction by using a model. It provides reports and analysis of the emotions expressed by the customer during conversations. Using the Model View Template (MVT) approach, the Emotion monitoring system is scalable, reusable and modular.

scholarly journals Mapping the impact of papers on various status groups in excellencemapping.net: a new release of the excellence mapping tool based on citation and reader scores

2021 ◽  
Author(s):  
Lutz Bornmann ◽  
Rüdiger Mutz ◽  
Robin Haunschild ◽  
Felix de Moya-Anegon ◽  
Mirko de Almeida Madeira Clemente ◽  
...  
Keyword(s):  
Web Application ◽  
Citation Data ◽  
Impact Measurement ◽  
Link Type ◽  
Mapping Tool ◽  
Institutional Impact ◽  
Institutional Profile ◽  
The Impact ◽  
The Web

AbstractIn over five years, Bornmann, Stefaner, de Moya Anegon, and Mutz (2014b) and Bornmann, Stefaner, de Moya Anegón, and Mutz (2014c, 2015) have published several releases of the www.excellencemapping.net tool revealing (clusters of) excellent institutions worldwide based on citation data. With the new release, a completely revised tool has been published. It is not only based on citation data (bibliometrics), but also Mendeley data (altmetrics). Thus, the institutional impact measurement of the tool has been expanded by focusing on additional status groups besides researchers such as students and librarians. Furthermore, the visualization of the data has been completely updated by improving the operability for the user and including new features such as institutional profile pages. In this paper, we describe the datasets for the current excellencemapping.net tool and the indicators applied. Furthermore, the underlying statistics for the tool and the use of the web application are explained.

scholarly journals Varapp: A reactive web-application for variants filtering

2016 ◽  
Author(s):  
Julien Delafontaine ◽  
Alexandre Masselot ◽  
Robin Liechti ◽  
Dmitry Kuznetsov ◽  
Ioannis Xenarios ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Web Application ◽  
De Novo ◽  
Source Code ◽  
Regions Of Interest ◽  
Mendelian Diseases ◽  
Link Type ◽  
Large Sets ◽  
Front End

AbstractSummary: Varapp is an open-source web application to filter variants from large sets of exome data stored in a relational database. Varapp offers a reactive graphical user interface, very fast data pro-cessing, security and facility to save, reproduce and shareresults. Typically, a few seconds suffice to apply non-trivial filters to a set of half a million variants and extract a handful of potential clinically relevant targets. Varapp implements different scenarios for Mendelian diseases (dominant, recessive, de novo, X-linked, andcompound heterozygous), and allows searching for variants in genes or chro-mosomal regions of interest.Availability: The application is made of a Javascript front-end and a Python back-end. Its source code is hosted at https://github.com/varapp. A demo version isavailable at https://varapp-demo.vital-it.ch. The full documentation can be found at https://varapp-demo.vital-it.ch/docs.Contact:[email protected]

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