scholarly journals VSIM: Visualization and simulation of variants in personal genomes with an application to premarital testing

2019 ◽  
Author(s):  
Azza Althagafi ◽  
Robert Hoehndorf
Keyword(s):  
Genetic Counseling ◽  
Research Group ◽  
Web Application ◽  
Background Knowledge ◽  
Personal Genome ◽  
Web Based ◽  
Genomic Features ◽  
Machine Learning Methods ◽  
Personal Genomes ◽  
Visualization And Simulation

AbstractBackgroundInterpretation of personal genomics data, for example in genetic counseling, is challenging due to the complexity of the data and the amount of background knowledge required for its interpretation. This background knowledge is distributed across several databases. Further information about genomic features can also be predicted through machine learning methods. Making this information accessible more easily has the potential to improve interpretation of variants in personal genomes.ResultsWe have developed VSIM, a web application for the interpretation and visualization of variants in personal genome sequences. VSIM identifies disease variants related to Mendelian, complex, and digenic disease as well as pharmacogenomic variants in personal genomes and visualizes them using a webserver. VSIM can further be used to simulate populations of children based on two parent genomes, and can be applied to support premarital genetic counseling. We make VSIM available as source code as well as through a container that can be installed easily in network environments in which genomic data is specially protected. VSIM and related documentation is freely available athttps://github.com/bio-ontology-research-group/VSIM.ConclusionsVSIM is a software that provides a web-based interface to variant interpretation in genetic counseling. VSIM can also be used for premarital genetic screening by simulating a population of children and analyze the disorder they might be carrying.

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.

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 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.

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.

scholarly journals Algorithm for detecting attacks on Web applications based on machine learning methods and attributes queries

2022 ◽  
Vol 2 (14) ◽  
pp. 26-34
Author(s):  
Nguyen Manh Thang ◽  
Tran Thi Luong
Keyword(s):  
Machine Learning ◽  
Web Application ◽  
Cloud Storage ◽  
Web Applications ◽  
Detection Algorithm ◽  
Learning Methods ◽  
Google Docs ◽  
Effective Work ◽  
Web Resources ◽  
Machine Learning Methods

Abstract—Almost developed applications tend to become as accessible as possible to the user on the Internet. Different applications often store their data in cyberspace for more effective work and entertainment, such as Google Docs, emails, cloud storage, maps, weather, news,... Attacks on Web resources most often occur at the application level, in the form of HTTP/HTTPS-requests to the site, where traditional firewalls have limited capabilities for analysis and detection attacks. To protect Web resources from attacks at the application level, there are special tools - Web Application Firewall (WAF). This article presents an anomaly detection algorithm, and how it works in the open-source web application firewall ModSecurity, which uses machine learning methods with 8 suggested features to detect attacks on web applications. Tóm tắt—Hầu hết các ứng dụng được phát triển có xu hướng trở nên dễ tiếp cận nhất có thể đối với người dùng qua Internet. Các ứng dụng khác nhau thường lưu trữ dữ liệu trên không gian mạng để làm việc và giải trí hiệu quả hơn, chẳng hạn như Google Docs, email, lưu trữ đám mây, bản đồ, thời tiết, tin tức,... Các cuộc tấn công vào tài nguyên Web thường xảy ra nhất ở tầng ứng dụng, dưới dạng các yêu cầu HTTP/HTTPS đến trang web, nơi tường lửa truyền thống có khả năng hạn chế trong việc phân tích và phát hiện các cuộc tấn công. Để bảo vệ tài nguyên Web khỏi các cuộc tấn công ở tầng ứng dụng, xuất hiện các công cụ đặc biệt - Tường lửa Ứng dụng Web (WAF). Bài viết này trình bày thuật toán phát hiện bất thường và cách thức hoạt động của tường lửa ứng dụng web mã nguồn mở ModSecurity khi sử dụng phương pháp học máy với 8 đặc trưng được đề xuất để phát hiện các cuộc tấn công vào các ứng dụng web.

scholarly journals Usability Assessment for the Enhancement of Quality of a Web Portal Interface

2019 ◽  
Vol 9 (1) ◽  
pp. 1636-1640
Keyword(s):  
Research Group ◽  
Single Point ◽  
Portal System ◽  
Web Portal ◽  
Web Based ◽  
Academic Administration ◽  
Usability Assessment ◽  
Wide Range ◽  
Applied Informatics

A web portal can be defined as a personalized, single point of access to information, resources and services covering a wide range of topic. Based on some researches, a system based on the internet can improve the work efficiency to some extent and provide all kinds of academic administration information timely. As to establish the intended function, usability is a crucial factor to be embarked on. This will ensure that the users are attracted to use the portal by increasing the relationship between the users and the portal’s interface. The Applied Informatics Research Group (AIRG) is the group assigned by the Faculty of Computer Science and Information Technology (FSKTM) to manage the Research Group Portal System (RGPS) that is the sample used in this research. The RGPS is a web-based system that allows collaboration among the users; to locate, store, use and share their knowledge. The main objective of this research is to obtain the feedbackfrom the users regarding the usability of the RGPS that is deterring them from optimizing the usage of this system. Surveys and questionnaires are used to evaluate and the output acts an input to modify the interface of the RGPS. Again, validation will be done to weight the users’ experience with the modified user interface.

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]

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