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>

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>

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):  
Electron Transfer ◽  
User Interface ◽  
Web Application ◽  
Shortest Paths ◽  
Coarse Grained ◽  
Electron Hole ◽  
Web Based ◽  
Aromatic Amino Acid Residue ◽  
Pathways Model ◽  
Visualization Tools

<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 with only through-space tunneling between electron transfer active (ETA) moieties being taken into account. 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>

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):  
Electron Transfer ◽  
User Interface ◽  
Amino Acid ◽  
Web Application ◽  
Shortest Paths ◽  
Coarse Grained ◽  
Electron Hole ◽  
Web Based ◽  
Aromatic Amino Acid Residue ◽  
Visualization Tools

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 <i>Pathways</i> model with only through-space tunneling between electron transfer active (ETA) moieties being taken into account. 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.

ANALYZING AND IMPROVING WEB APPLICATION QUALITY USING DESIGN PATTERNS

2012 ◽  
Vol 2 (2) ◽  
pp. 112-116
Author(s):  
Shikha Bhatia ◽  
Mr. Harshpreet Singh
Keyword(s):  
Web Application ◽  
Design Pattern ◽  
Design Patterns ◽  
Web Applications ◽  
Past Research ◽  
Software Systems ◽  
Interactive Software ◽  
Web Based ◽  
Software Application ◽  
Execution Speed

With the mounting demand of web applications, a number of issues allied to its quality have came in existence. In the meadow of web applications, it is very thorny to develop high quality web applications. A design pattern is a general repeatable solution to a generally stirring problem in software design. It should be noted that design pattern is not a finished product that can be directly transformed into source code. Rather design pattern is a depiction or template that describes how to find solution of a problem that can be used in many different situations. Past research has shown that design patterns greatly improved the execution speed of a software application. Design pattern are classified as creational design patterns, structural design pattern, behavioral design pattern, etc. MVC design pattern is very productive for architecting interactive software systems and web applications. This design pattern is partition-independent, because it is expressed in terms of an interactive application running in a single address space. We will design and analyze an algorithm by using MVC approach to improve the performance of web based application. The objective of our study will be to reduce one of the major object oriented features i.e. coupling between model and view segments of web based application. The implementation for the same will be done in by using .NET framework.

scholarly journals An Interactive Web Application for the Statistical Analysis of Continuous Glucose Monitoring Data in Epidemiological Studies

2021 ◽  
pp. 193229682098557
Author(s):  
Alysha M. De Livera ◽  
Jonathan E. Shaw ◽  
Neale Cohen ◽  
Anne Reutens ◽  
Agus Salim
Keyword(s):  
Continuous Glucose Monitoring ◽  
Web Application ◽  
Diabetes Management ◽  
Glucose Monitoring ◽  
Epidemiological Studies ◽  
Interactive Software ◽  
Web Based ◽  
Software Applications ◽  
Visualization Of Data ◽  
User Friendly

Motivation: Continuous glucose monitoring (CGM) systems are an essential part of novel technology in diabetes management and care. CGM studies have become increasingly popular among researchers, healthcare professionals, and people with diabetes due to the large amount of useful information that can be collected using CGM systems. The analysis of the data from these studies for research purposes, however, remains a challenge due to the characteristics and large volume of the data. Results: Currently, there are no publicly available interactive software applications that can perform statistical analyses and visualization of data from CGM studies. With the rapidly increasing popularity of CGM studies, such an application is becoming necessary for anyone who works with these large CGM datasets, in particular for those with little background in programming or statistics. CGMStatsAnalyser is a publicly available, user-friendly, web-based application, which can be used to interactively visualize, summarize, and statistically analyze voluminous and complex CGM datasets together with the subject characteristics with ease.

scholarly journals Preventive Measures for Cross Site Request Forgery Attacks on Web-based Applications

2018 ◽  
Vol 7 (4.15) ◽  
pp. 130
Author(s):  
Emil Semastin ◽  
Sami Azam ◽  
Bharanidharan Shanmugam ◽  
Krishnan Kannoorpatti ◽  
Mirjam Jonokman ◽  
...  
Keyword(s):  
Web Application ◽  
Web Applications ◽  
Operating Cycle ◽  
Web Application Security ◽  
Web Based ◽  
Business World ◽  
Application Security ◽  
Server Side ◽  
Combined Solution ◽  
Cross Site Request Forgery

Today’s contemporary business world has incorporated Web Services and Web Applications in its core of operating cycle nowadays and security plays a major role in the amalgamation of such services and applications with the business needs worldwide. OWASP (Open Web Application Security Project) states that the effectiveness of security mechanisms in a Web Application can be estimated by evaluating the degree of vulnerability against any of the nominated top ten vulnerabilities, nominated by the OWASP. This paper sheds light on a number of existing tools that can be used to test for the CSRF vulnerability. The main objective of the research is to identify the available solutions to prevent CSRF attacks. By analyzing the techniques employed in each of the solutions, the optimal tool can be identified. Tests against the exploitation of the vulnerabilities were conducted after implementing the solutions into the web application to check the efficacy of each of the solutions. The research also proposes a combined solution that integrates the passing of an unpredictable token through a hidden field and validating it on the server side with the passing of token through URL.  

Implementation of Web Application for Disease Prediction Using AI

2020 ◽  
pp. 5-9
Author(s):  
Manasvi Srivastava ◽  
◽  
Vikas Yadav ◽  
Swati Singh ◽  
◽  
...  
Keyword(s):  
Web Application ◽  
Ad Hoc ◽  
Data Extraction ◽  
Extraction Methods ◽  
Web Page ◽  
Web Based ◽  
Web Extraction ◽  
Web Scraping ◽  
Audio Video ◽  
Manual Extraction

The Internet is the largest source of information created by humanity. It contains a variety of materials available in various formats such as text, audio, video and much more. In all web scraping is one way. It is a set of strategies here in which we get information from the website instead of copying the data manually. Many Web-based data extraction methods are designed to solve specific problems and work on ad-hoc domains. Various tools and technologies have been developed to facilitate Web Scraping. Unfortunately, the appropriateness and ethics of using these Web Scraping tools are often overlooked. There are hundreds of web scraping software available today, most of them designed for Java, Python and Ruby. There is also open source software and commercial software. Web-based software such as YahooPipes, Google Web Scrapers and Firefox extensions for Outwit are the best tools for beginners in web cutting. Web extraction is basically used to cut this manual extraction and editing process and provide an easy and better way to collect data from a web page and convert it into the desired format and save it to a local or archive directory. In this paper, among others the kind of scrub, we focus on those techniques that extract the content of a Web page. In particular, we use scrubbing techniques for a variety of diseases with their own symptoms and precautions.

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.

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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