A Web-Based Tool for Visualization of Biomolecular Network Comparison

2014 ◽  
Vol 556-562 ◽  
pp. 5482-5487
Author(s):  
Hui Ran Zhang ◽  
Xiao Long Shen ◽  
Jiang Xie ◽  
Dong Bo Dai
Keyword(s):  
Open Source ◽  
Undirected Graphs ◽  
Web Based ◽  
Network Comparison ◽  
Biomolecular Networks ◽  
Biomolecular Network ◽  
Visualization Tools ◽  
Similarities And Differences ◽  
Adaptive Visualization

Analyzing similarities and differences between biomolecular networks comparison through website intuitively could be a convenient and effective way for researchers. Although several network comparison visualization tools have been developed, none of them can be integrated into websites. In this paper, a web-based tool kit named dynamically adaptive Visualization of Biomolecular Network Comparison (Bio-NCV) is designed and developed. The proposed tool is based on Cytyoscape.js – a popular open-source library for analyzing and visualizing networks. Bio-NCV integrates arjor.js which including the Barnes-Hut algorithm and the Traer Physics library for processing in order to express the dynamically adaptive initialization. In addition, in order to maintain consistency, the counterparts in other networks will change while the nodes and edges in one of the compared networks change. Furthermore, Bio-NCV can deal with both directed and undirected graphs.

Web Based GIS Application using Open Source Software for Sharing Geospatial Data

2015 ◽  
Vol 4 (1) ◽  
pp. 1224-1228 ◽  
Author(s):  
Debasish Chakraborty ◽  
◽  
Debanjan Sarkar ◽  
Shubham Agarwal ◽  
Dibyendu Dutta ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Geospatial Data ◽  
Web Based ◽  
Gis Application

eMap: A Web Application for Identifying and Visualizing Electron or Hole Hopping Pathways in Proteins

2019 ◽  
Author(s):  
Ruslan N. Tazhigulov ◽  
James R. Gayvert ◽  
Melissa Wei ◽  
Ksenia B. Bravaya
Keyword(s):  
Web Application ◽  
Shortest Paths ◽  
Coarse Grained ◽  
Decay Parameter ◽  
Electron Hole ◽  
Web Based ◽  
Aromatic Amino Acid Residue ◽  
Pathways Model ◽  
Visualization Tools ◽  
Effective Decay

<p>eMap is a web-based platform for identifying and visualizing electron or hole transfer pathways in proteins based on their crystal structures. The underlying model can be viewed as a coarse-grained version of the Pathways model, where each tunneling step between hopping sites represented by electron transfer active (ETA) moieties is described with one effective decay parameter that describes protein-mediated tunneling. ETA moieties include aromatic amino acid residue side chains and aromatic fragments of cofactors that are automatically detected, and, in addition, electron/hole residing sites that can be specified by the users. The software searches for the shortest paths connecting the user-specified electron/hole source to either all surface-exposed ETA residues or to the user-specified target. The identified pathways are ranked based on their length. The pathways are visualized in 2D as a graph, in which each node represents an ETA site, and in 3D using available protein visualization tools. Here, we present the capability and user interface of eMap 1.0, which is available at https://emap.bu.edu.</p>

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.

SigPrep: Open Source Web-Based Prework for Signals and Systems [SP Education]

2020 ◽  
Vol 37 (6) ◽  
pp. 184-191
Author(s):  
Utku Demir ◽  
Gaurav Sharma
Keyword(s):  
Open Source ◽  
Web Based

scholarly journals Short-term adoption rates for a web-based portal within the intranet of a hospital information system

2019 ◽  
Vol 26 (1) ◽  
pp. e100004 ◽  
Author(s):  
Athanasios Kotoulas ◽  
Ioannis Stratis ◽  
Theodoros Goumenidis ◽  
George Lambrou ◽  
Dimitrios - Dionysios Koutsouris
Keyword(s):  
Open Source ◽  
Resistance To Change ◽  
Content Management ◽  
Healthcare Management ◽  
Short Term ◽  
Web Based ◽  
Average Growth ◽  
Greek Hospital ◽  
Set Up ◽  
Free Open Source

ObjectiveAn intranet portal that combines cost-free, open-source software technology with easy set-up features can be beneficial for daily hospital processes. We describe the short-term adoption rates of a costless content management system (CMS) in the intranet of a tertiary Greek hospital.DesignDashboard statistics of our CMS platform were the implementation assessment of our system.ResultsIn a period of 10 months of running the software, the results indicate the employees overcame ‘Resistance to Change’ status. The average growth rate of end users who exploit the portal services is calculated as 2.73 every 3.3 months.ConclusionWe found our intranet web-based portal to be acceptable and helpful so far. Exploitation of an open-source CMS within the hospital intranet can influence healthcare management and the employees’ way of working as well.

scholarly journals Sa1099 Collection of Patient Centered Outcomes in Esophageal Disease: An Open Source Web Based Framework

2013 ◽  
Vol 144 (5) ◽  
pp. S-201-S-202
Author(s):  
Andrew J. Gawron ◽  
Sherri L. LaVela ◽  
David Were ◽  
Meghan Thompson ◽  
Jordan Swiskow ◽  
...  
Keyword(s):  
Open Source ◽  
Esophageal Disease ◽  
Patient Centered ◽  
Web Based

scholarly journals An Open-Source Web-Based Tool for Resource-Agnostic Interactive Translation Prediction

2014 ◽  
Vol 102 (1) ◽  
pp. 69-80 ◽  
Author(s):  
Torregrosa Daniel ◽  
Forcada Mikel L. ◽  
Pérez-Ortiz Juan Antonio
Keyword(s):  
Open Source ◽  
Machine Translation ◽  
Web Application ◽  
Statistical Machine Translation ◽  
Black Box ◽  
Translation System ◽  
Web Tool ◽  
Web Based ◽  
Strongly Coupled ◽  
Machine Translation System

Abstract We present a web-based open-source tool for interactive translation prediction (ITP) and describe its underlying architecture. ITP systems assist human translators by making context-based computer-generated suggestions as they type. Most of the ITP systems in literature are strongly coupled with a statistical machine translation system that is conveniently adapted to provide the suggestions. Our system, however, follows a resource-agnostic approach and suggestions are obtained from any unmodified black-box bilingual resource. This paper reviews our ITP method and describes the architecture of Forecat, a web tool, partly based on the recent technology of web components, that eases the use of our ITP approach in any web application requiring this kind of translation assistance. We also evaluate the performance of our method when using an unmodified Moses-based statistical machine translation system as the bilingual resource.

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