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.

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):  
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>

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.

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.

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 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.  

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.

STM3: a chemistry visualization platform

2005 ◽  
Vol 220 (5/6) ◽  
Author(s):  
Mario Valle
Keyword(s):  
User Interface ◽  
New Technologies ◽  
Software Platform ◽  
Visualization Tools ◽  
Visualization Techniques

AbstractTo support CSCS research users we built STM3, a software platform on which advanced chemistry visualization techniques can be integrated. Its main goal is not to replace existing tools, but to provide functionalities not covered by them. STM3’s unusual characteristic among chemistry visualization tools is its ability to combine chemistry and general visualization techniques in the same view. STM3 is built on top of a proven visualization environment (AVS/Express) that lets CSCS’s visualization staff concentrate its efforts on developing new technologies rather than investing time on graphical and user interface implementation issues.

Sign in / Sign up

Export Citation Format

Share Document