scholarly journals miRcomp-Shiny: Interactive assessment of qPCR-based microRNA quantification and quality control algorithms

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 2046 ◽  
Author(s):  
Lauren Kemperman ◽  
Matthew N. McCall
Keyword(s):  
Web Application ◽  
Performance Assessments ◽  
Estimation Methods ◽  
Quality Estimation ◽  
Data Set ◽  
Estimation Algorithms ◽  
Bioconductor Project ◽  
R Shiny ◽  
The Web ◽  
Shiny Application

The miRcomp-Shiny web application allows interactive performance assessments and comparisons of qPCR-based microRNA expression and quality estimation methods using a benchmark data set. This work is motivated by two distinct use cases: (1) selection of methodology and quality thresholds for use analyzing one's own data, and (2) comparison of novel expression estimation algorithms with currently-available methodology. The miRcomp-Shiny application is implemented in the R/Shiny language and can be installed on any operating system on which R can be installed. It is made freely available as part of the miRcomp package (version 1.3.3 and later) available through the Bioconductor project at: http://bioconductor.org/packages/miRcomp. The web application is hosted at https://laurenkemperman.shinyapps.io/mircomp/. A detailed description of how to use the web application is available at: http://lkemperm.github.io/miRcomp_shiny_app

scholarly journals Building the Security Function Point Method for Web Application Vulnerability Remediation

2019 ◽  
Vol 8 (4) ◽  
pp. 5962-5968
Keyword(s):  
Web Application ◽  
Model Development ◽  
Point Method ◽  
Estimation Methods ◽  
Resource Estimation ◽  
Corporate Security ◽  
Function Point ◽  
Vulnerability Framework ◽  
Project Data ◽  
The Web

The web application vulnerability remediation activities are important in terms of actual risk management in corporate security activities. However, traditional software development resource estimation methods do not discuss resource estimation for software vulnerability remediation in terms of security. Moreover, it is difficult to estimate the exact web vulnerability remediation resources using correction factors. In these backgrounds this study aims to establish a resource estimation methodology for web application vulnerability remediation in terms of security from the perspective of dynamic analysis, contributing to foundation building for the systematic management of web application vulnerability remediation among information security organizations and related practitioners. For the new model development, this study used 64 application data of the experimental company to derive the security function point method and 6 web vulnerability assessment project data from the same company to verify the methodology.Hence a web application vulnerability remediation standard was established, and a new security web vulnerability remediation resource estimation technique, “Security Function Point Method (SFPM),” was proposed through data collection based on the standard.It covers the de facto global web application vulnerability framework named OWASP Top 10(2017) and several Korea’s standards fromthe practical field. Thus, it is possible tocalculate the web application vulnerability remediation resourcesin a better way

scholarly journals GMIEC: a shiny application for the identification of gene-targeted drugs for precision medicine

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Guidantonio Malagoli Tagliazucchi ◽  
Cristian Taccioli
Keyword(s):  
Precision Medicine ◽  
Copy Number ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Data Set ◽  
Cancer Data ◽  
R Shiny ◽  
Number Variation ◽  
New Treatments ◽  
Shiny Application

Abstract Background Precision medicine is a medical approach that takes into account individual genetic variability and often requires Next Generation Sequencing data in order to predict new treatments. Here we present GMIEC, Genomic Modules Identification et Characterization for genomics medicine, an application that is able to identify specific drugs at the level of single patient integrating multi-omics data such as RNA-sequencing, copy-number variation, methylation, Chromatin Immuno-Precipitation and Exome/Whole Genome sequencing. It is also possible to include clinical data related to each patient. GMIEC has been developed as a web-based R-Shiny platform and gives as output a table easy to use and explore. Results We present GMIEC, a Shiny application for genomics medicine. The tool allows the users the integration of two or more multiple omics datasets (e.g. gene-expression, copy-number), at sample level, to identify groups of genes that share common genomic and corresponding drugs. We demonstrate the characteristics of our application by using it to analyze a prostate cancer data set. Conclusions GMIEC provides a simple interface for genomics medicine. GMIEC was develop with Shiny to provide an application that does not require advanced programming skills. GMIEC consists of three sub-application for the analysis (GMIEC-AN), the visualization (GMIEC-VIS) and the exploration of results (GMIEC-RES). GMIEC is an open source software and is available at https://github.com/guidmt/GMIEC-shiny

scholarly journals A large-scale transcriptome-wide association study (TWAS) of ten blood cell phenotypes reveals complexities of TWAS fine-mapping

2021 ◽  
Author(s):  
Amanda L Tapia ◽  
Bryce T Rowland ◽  
Jonathan D Rosen ◽  
Michael Preuss ◽  
Kris Young ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fine Mapping ◽  
Web Application ◽  
Large Scale ◽  
Association Studies ◽  
Regulatory Mechanisms ◽  
European Ancestry ◽  
R Shiny ◽  
Hematological Measures ◽  
Shiny Application

AbstractHematological measures are important intermediate clinical phenotypes for many acute and chronic diseases. Hematological measures are highly heritable, and although genome-wide association studies (GWAS) have identified thousands of loci containing trait-associated variants, the causal genes underlying these associations are often uncertain. To better understand the underlying genetic regulatory mechanisms, we performed a transcriptome-wide association study (TWAS) using PrediXcan to systematically investigate the association between genetically-predicted gene expression and hematological measures in 54,542 individuals of European ancestry from the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. We found 239 significant gene-trait associations with hematological measures. Among this set of 239 associations, we replicated 71 at p < 0.05 with same direction of effect for the blood cell trait in a meta-analysis of TWAS results consisting of up to 35,900 European ancestry individuals from the Women’s Health Initiative (WHI), the Atherosclerosis Risk in Communities Study (ARIC), and BioMe Biobank. We further attempted to refine this list of candidate genes by performing conditional analyses, adjusting for individual variants previously associated with these hematological measures, and performed further fine-mapping of TWAS loci. To assist with the interpretation of TWAS findings, we designed an R Shiny application to interactively visualize TWAS results, one genomic locus at a time, by integrating our TWAS results with additional genetic data sources (GWAS, TWAS from other gene expression reference panels, conditional analyses, known GWAS variants, etc.). Our results and R Shiny application highlight frequently overlooked challenges with TWAS and illustrate the complexity of TWAS fine-mapping efforts.Author SummaryTranscriptome-wide association studies (TWAS) have shown great promise in furthering our understanding of the genetic regulatory mechanisms underlying complex trait variation. However, interpreting TWAS results can be incredibly complex, especially in large-scale analyses where hundreds of signals appear throughout the genome, with multiple genes often identified in a single chromosomal region. Our research demonstrates this complexity through real data examples from our analysis of hematological traits, and we provide a useful web application to visualize TWAS results in a broadly approachable format. Together, our results and web application illustrate the importance of interpreting TWAS studies in context and highlight the need to carefully examine results in a region-wide context to draw reasonable conclusions and formulate mechanistic hypotheses.

scholarly journals A hybrid of CNN and LSTM methods for securing web application against cross-site scripting attack

2021 ◽  
Vol 21 (2) ◽  
pp. 1022
Author(s):  
Raed Waheed Kadhim ◽  
Methaq Talib Gaata
Keyword(s):  
Neural Network ◽  
Web Application ◽  
Web Applications ◽  
Excellent Result ◽  
Test Word ◽  
Short Term ◽  
Data Set ◽  
Proposed Model ◽  
Cross Site ◽  
The Web

<span>Cross-site scripting (XSS) is today one of the biggest threatthat could targeting the Web application. Based on study published by the open web applications security project (OWASP), XSS vulnerability has been present among the TOP 10 Web application vulnerabilities.Still,an important security-related issue remains how to effectively protect web applications from XSS attacks.In first part of this paper, a method for detecting XSS attack was proposed by combining </span><span lang="EN-GB">convolutional</span><span> neural network (CNN) with long short term memories<strong> (</strong>LSTM), Initially, pre-processing was applied to XSS Data Set by decoding, generalization and tokanization, and then word2vec was applied to convert words into word vectors in XSS payloads. And then we use the combination CNN with LSTM to train and test word vectors to produce a model that can be used in a web application. Based on the obtaned results, it is observed that the proposed model achevied an excellent result with accuracy of 99.4%.</span>

THE USE OF WEB APPLICATIONS FOR THE SELECTION OF CROP GROWING TECHNOLOGIES

2018 ◽  
Vol 48 (3) ◽  
pp. 84-90 ◽  
Author(s):  
E. A. Lapchenko ◽  
S. P. Isakova ◽  
T. N. Bobrova ◽  
L. A. Kolpakova
Keyword(s):  
Web Application ◽  
Crop Production ◽  
Web Applications ◽  
Weather Forecast ◽  
Technical Institute ◽  
Software Complex ◽  
Agricultural Enterprise ◽  
Weather Situation ◽  
The Web ◽  
Selection Of

It is shown that the application of the Internet technologies is relevant in the selection of crop production technologies and the formation of a rational composition of the machine-and-tractor fl eet taking into account the conditions and production resources of a particular agricultural enterprise. The work gives a short description of the web applications, namely “ExactFarming”, “Agrivi” and “AgCommand” that provide a possibility to select technologies and technical means of soil treatment, and their functions. “ExactFarming” allows to collect and store information about temperature, precipitation and weather forecast in certain areas, keep records of information about crops and make technological maps using expert templates. “Agrivi” allows to store and provide access to weather information in the fi elds with certain crops. It has algorithms to detect and make warnings about risks related to diseases and pests, as well as provides economic calculations of crop profi tability and crop planning. “AgCommand” allows to track the position of machinery and equipment in the fi elds and provides data on the weather situation in order to plan the use of agricultural machinery in the fi elds. The web applications presented hereabove do not show relation between the technologies applied and agro-climatic features of the farm location zone. They do not take into account the phytosanitary conditions in the previous years, or the relief and contour of the fi elds while drawing up technological maps or selecting the machine-and-tractor fl eet. Siberian Physical-Technical Institute of Agrarian Problems of Siberian Federal Scientifi c Center of AgroBioTechnologies of the Russian Academy of Sciences developed a software complex PIKAT for supporting machine agrotechnologies for production of spring wheat grain at an agricultural enterprise, on the basis of which there is a plan to develop a web application that will consider all the main factors limiting the yield of cultivated crops.

Spring Framework for Testing

2020 ◽  
Author(s):  
Darshak Mota ◽  
Neel Zadafiya ◽  
Jinan Fiaidhi
Keyword(s):  
Web Application ◽  
Application Development ◽  
Spring Framework ◽  
Java Application ◽  
Development Framework ◽  
Development Life Cycle ◽  
Form Model ◽  
Project Structure ◽  
Model View ◽  
The Web

Java Spring is an application development framework for enterprise Java. It is an open source platform which is used to develop robust Java application easily. Spring can also be performed using MVC structure. The MVC architecture is based on Model View and Controller techniques, where the project structure or code is divided into three parts or sections which helps to categorize the code files and other files in an organized form. Model, View and Controller code are interrelated and often passes and fetches information from each other without having to put all code in a single file which can make testing the program easy. Testing the application while and after development is an integral part of the Software Development Life Cycle (SDLC). Different techniques have been used to test the web application which is developed using Java Spring MVC architecture. And compares the results among all the three different techniques used to test the web application.

Evaluation for estimating of the PDF and the CDF of Generalized Inverted Exponential Distribution with Application in Industry

2020 ◽  
pp. 507-522
Author(s):  
Parisa Torkaman
Keyword(s):  
Least Squares ◽  
Exponential Distribution ◽  
Mean Squared Error ◽  
Weighted Least Squares ◽  
Real Data ◽  
Minimum Variance ◽  
Cumulative Distribution ◽  
Estimation Methods ◽  
Data Set ◽  
Better Than

The generalized inverted exponential distribution is introduced as a lifetime model with good statistical properties. This paper, the estimation of the probability density function and the cumulative distribution function of with five different estimation methods: uniformly minimum variance unbiased(UMVU), maximum likelihood(ML), least squares(LS), weighted least squares (WLS) and percentile(PC) estimators are considered. The performance of these estimation procedures, based on the mean squared error (MSE) by numerical simulations are compared. Simulation studies express that the UMVU estimator performs better than others and when the sample size is large enough the ML and UMVU estimators are almost equivalent and efficient than LS, WLS and PC. Finally, the result using a real data set are analyzed.

Properties and methods of estimation for a bivariate exponentiated Fréchet distribution

2020 ◽  
Vol 70 (5) ◽  
pp. 1211-1230
Author(s):  
Abdus Saboor ◽  
Hassan S. Bakouch ◽  
Fernando A. Moala ◽  
Sheraz Hussain
Keyword(s):  
Maximum Likelihood ◽  
Probability Density Function ◽  
Probability Density ◽  
Density Function ◽  
Superior Performance ◽  
Estimation Methods ◽  
Conditional Probability Density ◽  
Data Set ◽  
Fréchet Distribution ◽  
Frechet Distribution

AbstractIn this paper, a bivariate extension of exponentiated Fréchet distribution is introduced, namely a bivariate exponentiated Fréchet (BvEF) distribution whose marginals are univariate exponentiated Fréchet distribution. Several properties of the proposed distribution are discussed, such as the joint survival function, joint probability density function, marginal probability density function, conditional probability density function, moments, marginal and bivariate moment generating functions. Moreover, the proposed distribution is obtained by the Marshall-Olkin survival copula. Estimation of the parameters is investigated by the maximum likelihood with the observed information matrix. In addition to the maximum likelihood estimation method, we consider the Bayesian inference and least square estimation and compare these three methodologies for the BvEF. A simulation study is carried out to compare the performance of the estimators by the presented estimation methods. The proposed bivariate distribution with other related bivariate distributions are fitted to a real-life paired data set. It is shown that, the BvEF distribution has a superior performance among the compared distributions using several tests of goodness–of–fit.

scholarly journals A Sign of Things to Come: Predicting the Perception of Above-the-Fold Time in Web Browsing

2021 ◽  
Vol 13 (2) ◽  
pp. 50
Author(s):  
Hamed Z. Jahromi ◽  
Declan Delaney ◽  
Andrew Hines
Keyword(s):  
Web Application ◽  
Web Applications ◽  
State Of The Art ◽  
Influencing Factor ◽  
The State ◽  
Experimental Result ◽  
Web Page ◽  
To Come ◽  
Web Quality ◽  
The Web

Content is a key influencing factor in Web Quality of Experience (QoE) estimation. A web user’s satisfaction can be influenced by how long it takes to render and visualize the visible parts of the web page in the browser. This is referred to as the Above-the-fold (ATF) time. SpeedIndex (SI) has been widely used to estimate perceived web page loading speed of ATF content and a proxy metric for Web QoE estimation. Web application developers have been actively introducing innovative interactive features, such as animated and multimedia content, aiming to capture the users’ attention and improve the functionality and utility of the web applications. However, the literature shows that, for the websites with animated content, the estimated ATF time using the state-of-the-art metrics may not accurately match completed ATF time as perceived by users. This study introduces a new metric, Plausibly Complete Time (PCT), that estimates ATF time for a user’s perception of websites with and without animations. PCT can be integrated with SI and web QoE models. The accuracy of the proposed metric is evaluated based on two publicly available datasets. The proposed metric holds a high positive Spearman’s correlation (rs=0.89) with the Perceived ATF reported by the users for websites with and without animated content. This study demonstrates that using PCT as a KPI in QoE estimation models can improve the robustness of QoE estimation in comparison to using the state-of-the-art ATF time metric. Furthermore, experimental result showed that the estimation of SI using PCT improves the robustness of SI for websites with animated content. The PCT estimation allows web application designers to identify where poor design has significantly increased ATF time and refactor their implementation before it impacts end-user experience.

scholarly journals Psychometric properties of a self-assessment questionnaire concerning symptoms and impairment in urinary tract infections: the UTI-SIQ-8

BMJ Open ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. e043328
Author(s):  
Ildikó Gágyor ◽  
Katrin Rentzsch ◽  
Stephanie Strube-Plaschke ◽  
Wolfgang Himmel
Keyword(s):  
Primary Care ◽  
Urinary Tract ◽  
Psychometric Properties ◽  
Symptom Severity ◽  
Web Application ◽  
Sensitivity To Change ◽  
Observation Study ◽  
Tract Infections ◽  
Daily Changes ◽  
The Web

ObjectivesTo validate the urinary tract infection-Symptom and Impairment Questionnaire (UTI-SIQ-8), a questionnaire that consists of four items to assess the symptom severity for dysuria, urgency, frequenc, and low abdominal pain and four items to assess the resulting impairment of activity by UTIs.DesignProspective observation study.SettingGerman primary care practices.ParticipantsAn unselected population of women with UTI. Women could participate online via a web application for smartphones, smartwatches and tablets or use a paper-and-pencil version.Main outcomesPsychometric properties of the UTI-SIQ-8 regarding reliability, validity and sensitivity to change by using factor analysis and multilevel and network analysis.ResultsData from 120 women with a total of 769 symptom reports across 7 days of measurement were analysed. The majority of the participating patients (87/120) used the web application via smartphones or other devices. The reliability of the UTI-SIQ-8 was high, with Cronbach’s alpha of .86 at intake; convergent and discriminant validity was satisfactory. Intraclass correlation demonstrated high sensitivity to change, with 68% of the total variance being due to time differences. These daily changes in an individual’s symptoms moved parallel with daily changes in the EQ-5D-5L (b=1.68, SE=0.12, p<0.001) and the visual analogue scale (b=0.03, SE=0.003, p<0.001), also highlighting convergent validity with respect to daily changes in symptom severity.ConclusionsThe present findings support the UTI-SIQ-8 questionnaire as an economic, reliable and valid instrument for the assessment of symptom severity and symptom change in women with uncomplicated UTI. The web application helped patients to report symptoms on a daily basis. These findings may encourage primary care physicians to use the UTI-SIQ-8 in their daily practice and researchers to apply it to studies involving patients with uncomplicated UTI.

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