scholarly journals KinderMiner Web: a simple web tool for ranking pairwise associations in biomedical applications

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 832
Author(s):  
Finn Kuusisto ◽  
Daniel Ng ◽  
John Steill ◽  
Ian Ross ◽  
Miron Livny ◽  
...  
Keyword(s):  
Text Mining ◽  
Web Application ◽  
Biomedical Applications ◽  
Analysis Tool ◽  
Trial And Error ◽  
Web Tool ◽  
Interactive Analysis ◽  
Term List ◽  
Public Resource ◽  
The Web

Many important scientific discoveries require lengthy experimental processes of trial and error and could benefit from intelligent prioritization based on deep domain understanding. While exponential growth in the scientific literature makes it difficult to keep current in even a single domain, that same rapid growth in literature also presents an opportunity for automated extraction of knowledge via text mining. We have developed a web application implementation of the KinderMiner algorithm for proposing ranked associations between a list of target terms and a key phrase. Any key phrase and target term list can be used for biomedical inquiry. We built the web application around a text index derived from PubMed. It is the first publicly available implementation of the algorithm, is fast and easy to use, and includes an interactive analysis tool. The KinderMiner web application is a public resource offering scientists a cohesive summary of what is currently known about a particular topic within the literature, and helping them to prioritize experiments around that topic. It performs comparably or better to similar state-of-the-art text mining tools, is more flexible, and can be applied to any biomedical topic of interest. It is also continually improving with quarterly updates to the underlying text index and through response to suggestions from the community. The web application is available at https://www.kinderminer.org.

scholarly journals KinderMiner Web: a simple web tool for ranking pairwise associations in biomedical applications

F1000Research ◽  
2021 ◽  
Vol 9 ◽  
pp. 832
Author(s):  
Finn Kuusisto ◽  
Daniel Ng ◽  
John Steill ◽  
Ian Ross ◽  
Miron Livny ◽  
...  
Keyword(s):  
Text Mining ◽  
Web Application ◽  
Biomedical Applications ◽  
Analysis Tool ◽  
Trial And Error ◽  
Web Tool ◽  
Interactive Analysis ◽  
Term List ◽  
Public Resource ◽  
The Web

Many important scientific discoveries require lengthy experimental processes of trial and error and could benefit from intelligent prioritization based on deep domain understanding. While exponential growth in the scientific literature makes it difficult to keep current in even a single domain, that same rapid growth in literature also presents an opportunity for automated extraction of knowledge via text mining. We have developed a web application implementation of the KinderMiner algorithm for proposing ranked associations between a list of target terms and a key phrase. Any key phrase and target term list can be used for biomedical inquiry. We built the web application around a text index derived from PubMed. It is the first publicly available implementation of the algorithm, is fast and easy to use, and includes an interactive analysis tool. The KinderMiner web application is a public resource offering scientists a cohesive summary of what is currently known about a particular topic within the literature, and helping them to prioritize experiments around that topic. It performs comparably or better to similar state-of-the-art text mining tools, is more flexible, and can be applied to any biomedical topic of interest. It is also continually improving with quarterly updates to the underlying text index and through response to suggestions from the community. The web application is available at https://www.kinderminer.org.

scholarly journals The Web Application of Constitution Analysis System - SCAT (Sasang Constitution Analysis Tool) -

2016 ◽  
Vol 28 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Ji-Ho So ◽  
Jang-Woong Kim ◽  
Ji-Ho Nam ◽  
Bum-Ju Lee ◽  
Young-Su Kim ◽  
...  
Keyword(s):  
Web Application ◽  
Analysis Tool ◽  
Sasang Constitution ◽  
Analysis System ◽  
The Web

scholarly journals Web-tool for managing a set of testswith synchronization with moodle

2021 ◽  
Vol 17 (4) ◽  
pp. 95-99
Author(s):  
Sergey N. Shergin ◽  
Nikita V. Denisov ◽  
Viktor V. Luka
Keyword(s):  
Web Application ◽  
Web Tool ◽  
The Web

The article discusses a web application for creating, managing and structuring the bank (set) of tests. In the course of the work, a structured database was proposed, and the web application was optimized. The main goal is to take as a basis the current module for managing and creating a bank of test tasks of the moodle system and optimize it.

scholarly journals A Novel Multi-Risk Assessment Web-Tool for Evaluating Future Impacts of Global Change in Mountainous Areas

Climate ◽  
2018 ◽  
Vol 6 (4) ◽  
pp. 92 ◽  
Author(s):  
Gilles Grandjean ◽  
Loïc Thomas ◽  
Séverine Bernardie ◽  
The SAMCO Team
Keyword(s):  
Risk Assessment ◽  
Global Change ◽  
Web Application ◽  
Environmental Changes ◽  
Decision Support Tool ◽  
Web Tool ◽  
Support Tool ◽  
Hazard And Risk ◽  
Global Environmental Changes ◽  
The Web

In our study, we present a proactive decision support tool able to compute the impacts of different possible scenarios for territories impacted by mountain risks. The objective of this work was to develop and test various hazard and risk assessment methods, and to implement them into a web-application platform able to show possible risks induced by global change on ecosystems and society. Four case studies were selected for their representativeness: One located in a Pyrenean valley, others in the French Alps. Methodology addressed several points. The first one was on the identification of the impacts of global environmental changes (climatic situations, land use, and socio-economic systems) on identified hazards. The second one was on the analysis of these impacts in terms of vulnerability (e.g., the places and the physical modifications of impacted stakes, as well as levels of perturbation). The third one was on the integration of developed methodologies in a single coherent framework in order to investigate and map indicators of vulnerability. The last one was on the development of a demonstration platform with GIS (Geographic Information System) capabilities and usable on the web. The architecture and the main features of the web-platform are detailed within several cases for which hazard and impact assessments are evaluated for not only past and present, but also future periods. This web-tool, mostly dedicated to stakeholders, has proven its usefulness to test various socio-economical pathways, because multiple scenarios, considered as probable in inhabited valleys, can be benchmarked, analyzed, and compared.

scholarly journals SimText: A text mining framework for interactive analysis and visualization of similarities among biomedical entities

2020 ◽  
Author(s):  
Marie Gramm ◽  
Eduardo Pérez-Palma ◽  
Sarah Schumacher-Bass ◽  
Jarrod Dalton ◽  
Costin Leu ◽  
...  
Keyword(s):  
Text Mining ◽  
Web Application ◽  
Data Generation ◽  
R Software ◽  
Online Data ◽  
Interactive Analysis ◽  
Learning Techniques ◽  
User Friendly ◽  
Analysis Platform ◽  
Command Line Version

AbstractLiterature exploration in PubMed on a large number of biomedical entities (e.g., genes, diseases, experiments) can be time consuming and challenging comparing many entities to one other. Here, we describe SimText, a user-friendly toolset that provides customizable and systematic workflows for the analysis of similarities among a set of entities based on words from abstracts and/or other text. SimText can be used for (i) data generation: text collection from PubMed and extraction of words with different text mining approaches, and (ii) interactive analysis of data using unsupervised learning techniques and visualization in a Shiny web application.Availability and ImplementationWe developed SimText as an open-source R software and integrated it into Galaxy, an online data analysis platform. A command line version of the toolset is available for download from GitHub at https://github.com/mgramm1/simtext.

scholarly journals SynergyFinder 2.0: visual analytics of multi-drug combination synergies

2020 ◽  
Vol 48 (W1) ◽  
pp. W488-W493 ◽  
Author(s):  
Aleksandr Ianevski ◽  
Anil K Giri ◽  
Tero Aittokallio
Keyword(s):  
Drug Combination ◽  
Visual Analytics ◽  
Web Application ◽  
Model Systems ◽  
Web Tool ◽  
Clinical Model ◽  
Interactive Analysis ◽  
Potential Applications ◽  
And Performance ◽  
Replicate Measurements

Abstract SynergyFinder (https://synergyfinder.fimm.fi) is a stand-alone web-application for interactive analysis and visualization of drug combination screening data. Since its first release in 2017, SynergyFinder has become a widely used web-tool both for the discovery of novel synergistic drug combinations in pre-clinical model systems (e.g. cell lines or primary patient-derived cells), and for better understanding of mechanisms of combination treatment efficacy or resistance. Here, we describe the latest version of SynergyFinder (release 2.0), which has extensively been upgraded through the addition of novel features supporting especially higher-order combination data analytics and exploratory visualization of multi-drug synergy patterns, along with automated outlier detection procedure, extended curve-fitting functionality and statistical analysis of replicate measurements. A number of additional improvements were also implemented based on the user requests, including new visualization and export options, updated user interface, as well as enhanced stability and performance of the web-tool. With these improvements, SynergyFinder 2.0 is expected to greatly extend its potential applications in various areas of multi-drug combinatorial screening and precision medicine.

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.

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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