Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA

AbstractMicroRNAs (miRNAs) are important regulators of gene expression. The large-scale detection and profiling of miRNAs has accelerated with the development of high-throughput small RNA sequencing (sRNA-Seq) techniques and bioinformatics tools. However, generating high-quality comprehensive miRNA annotations remains challenging, due to the intrinsic complexity of sRNA-Seq data and inherent limitations of existing miRNA predictions. Here, we present iwa-miRNA, a Galaxy-based framework that can facilitate miRNA annotation in plant species by combining computational analysis and manual curation. iwa-miRNA is specifically designed to generate a comprehensive list of miRNA candidates, bridging the gap between already annotated miRNAs provided by public miRNA databases and new predictions from sRNA-Seq datasets. It can also assist users to select promising miRNA candidates in an interactive mode through the automated and manual steps, contributing to the accessibility and reproducibility of genome-wide miRNA annotation. iwa-miRNA is user-friendly and can be easily deployed as a web application for researchers without programming experience. With flexible, interactive, and easy-to-use features, iwa-miRNA is a valuable tool for annotation of miRNAs in plant species with reference genomes. We illustrated the application of iwa-miRNA for miRNA annotation of plant species with varying complexity. The sources codes and web server of iwa-miRNA is freely accessible at: http://iwa-miRNA.omicstudio.cloud/.

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The Framework for Web-Based Automated Online Question Paper Generator through JEE

International Journal of Engineering & Technology ◽

10.14419/ijet.v7i3.13573 ◽

2018 ◽

Vol 7 (3) ◽

pp. 1415

Author(s):

Vinayak Hegde ◽

Lavanya V Rao ◽

Shivali B S

Keyword(s):

Web Application ◽

Large Scale ◽

Educational Institution ◽

Faculty Members ◽

Educational Institutions ◽

Small Scale ◽

Web Based ◽

Educational Institute ◽

User Friendly ◽

Word Format

Examinations are an indispensable part of a student’s life. In the conventional mechanism, the question paper generation is time-consuming work for the faculty members of the educational institution. Every educational institute mandatorily expects exam setters to follow its own typesetting format. We have designed the automated question paper setting software to be user-friendly so that, paper setters can overcome from the typographic problem. Presently in most of the educational institutions question papers are set manually. It is time-consuming work and there may be chances of repetition of the same questions. So, in order to make the question paper generation more convenient to use, the web application is developed using Java Enterprise Edition (JEE) that can be accessed from LAN/Intranet.The application comes with the Admin Module and Teachers Module. The Admin grants access to the users by registering them. The faculty can access the system once they are registered. The faculty can enter questions in the database daily as per their free time. In this way, the question pool can be generated. The questions are approved by the chairperson and substandard questions are discarded. The question paper is then generated by selected course experts. The Fisher-Yates Shuffling algorithm used to choose questions randomly from the pool of questions from the database. Text Mining Algorithm aids in duplicity removal from the paper. The generated question paper will be in Word Format. In our application, we assure better security, removal of duplicity, cost-effectiveness, and human intervention avoidance. It can be used by small-scale and large-scale institutions.

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

Journal of Diabetes Science and Technology ◽

10.1177/1932296820985570 ◽

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.

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CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalk

10.1101/102848 ◽

2017 ◽

Author(s):

Venkata Manem ◽

George Adam ◽

Tina Gruosso ◽

Mathieu Gigoux ◽

Nicholas Bertos ◽

...

Keyword(s):

Stromal Cells ◽

Large Scale ◽

Network Visualization ◽

Visualization Tool ◽

Biological Processes ◽

Web Based ◽

Link Type ◽

A Cell ◽

Large Scale Networks ◽

User Friendly

ABSTRACTBackground:Over the last several years, we have witnessed the metamorphosis of network biology from being a mere representation of molecular interactions to models enabling inference of complex biological processes. Networks provide promising tools to elucidate intercellular interactions that contribute to the functioning of key biological pathways in a cell. However, the exploration of these large-scale networks remains a challenge due to their high-dimensionality.Results:CrosstalkNet is a user friendly, web-based network visualization tool to retrieve and mine interactions in large-scale bipartite co-expression networks. In this study, we discuss the use of gene co-expression networks to explore the rewiring of interactions between tumor epithelial and stromal cells. We show how CrosstalkNet can be used to efficiently visualize, mine, and interpret large co-expression networks representing the crosstalk occurring between the tumour and its microenvironment.Conclusion:CrosstalkNet serves as a tool to assist biologists and clinicians in exploring complex, large interaction graphs to obtain insights into the biological processes that govern the tumor epithelial-stromal crosstalk. A comprehensive tutorial along with case studies are provided with the application.Availability:The web-based application is available at the following location: http://epistroma.pmgenomics.ca/app/. The code is open-source and freely available from http://github.com/bhklab/EpiStroma-webapp.Contact:[email protected]

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G4Killer web application: a tool to design G-quadruplex mutations

Bioinformatics ◽

10.1093/bioinformatics/btaa057 ◽

2020 ◽

Vol 36 (10) ◽

pp. 3246-3247

Author(s):

Vaclav Brazda ◽

Jan Kolomaznik ◽

Jean-Louis Mergny ◽

Jiri Stastny

Keyword(s):

Dna Sequences ◽

Web Application ◽

Rational Design ◽

Therapeutic Potential ◽

Supplementary Information ◽

Web Tool ◽

Web Based ◽

Dna Structures ◽

G Quadruplex ◽

User Friendly

Abstract Motivation G-quadruplexes (G4) are important regulatory non-B DNA structures with therapeutic potential. A tool for rational design of mutations leading to decreased propensity for G4 formation should be useful in studying G4 functions. Although tools exist for G4 prediction, no easily accessible tool for the rational design of G4 mutations has been available. Results We developed a web-based tool termed G4Killer that is based on the G4Hunter algorithm. This new tool is a platform-independent and user-friendly application to design mutations crippling G4 propensity in a parsimonious way (i.e., keeping the primary sequence as close as possible to the original one). The tool is integrated into our DNA analyzer server and allows for generating mutated DNA sequences having the desired lowered G4Hunter score with minimal mutation steps. Availability and implementation The G4Killer web tool can be accessed at: http://bioinformatics.ibp.cz. Supplementary information Supplementary data are available at Bioinformatics online.

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epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology

Bioinformatics ◽

10.1093/bioinformatics/btz387 ◽

2019 ◽

Vol 35 (21) ◽

pp. 4462-4464

Author(s):

Jordan H Creed ◽

Garrick Aden-Buie ◽

Alvaro N Monteiro ◽

Travis A Gerke

Keyword(s):

Genetic Epidemiology ◽

In Silico ◽

Web Application ◽

Large Scale ◽

Source Code ◽

Chromosome Conformation Capture ◽

Chromosome Conformation ◽

Web Based ◽

Genome Wide ◽

Public Data

Abstract Summary Complementary advances in genomic technology and public data resources have created opportunities for researchers to conduct multifaceted examination of the genome on a large scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic 3D organization and annotations across multiple databases in an interactive manner to facilitate in silico discovery. Availability and implementation epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/ where we have additionally made publicly available the source code and a Docker containerized version of the application.

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lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720016500165 ◽

2016 ◽

Vol 14 (04) ◽

pp. 1650016 ◽

Cited By ~ 17

Author(s):

Ruifeng Hu ◽

Xiaobo Sun

Keyword(s):

Free Energy ◽

Nucleic Acid ◽

Large Scale ◽

Nearest Neighbor ◽

Binding Free Energy ◽

Target Prediction ◽

Easy Access ◽

Web Based ◽

Size Limitation ◽

User Friendly

Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. We provided lncRNATargets, which is a web-based platform for lncRNA target prediction based on nucleic acid thermodynamics. The nearest-neighbor (NN) model was used to calculate binging-free energy. The main principle of NN model for nucleic acid assumes that identity and orientation of neighbor base pairs determine stability of a given base pair. lncRNATargets features the following options: setting of a specific temperature that allow use not only for human but also for other animals or plants; processing all lncRNAs in high throughput without RNA size limitation that is superior to any other existing tool; and web-based, user-friendly interface, and colored result displays that allow easy access for nonskilled computer operators and provide better understanding of results. This technique could provide accurate calculation on the binding-free energy of lncRNA-target dimers to predict if these structures are well targeted together. lncRNATargets provides high accuracy calculations, and this user-friendly program is available for free at http://www.herbbol.org:8001/lrt/ .

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Data Browser Matsch | Mazia: Web Application to access microclimatic time series of an ecological research site

Research Ideas and Outcomes ◽

10.3897/rio.7.e63748 ◽

2021 ◽

Vol 7 ◽

Author(s):

Martin Palma ◽

Alessandro Zandonai ◽

Luca Cattani ◽

Johannes Klotz ◽

Giulio Genova ◽

...

Keyword(s):

Time Series ◽

Web Application ◽

Scientific Data ◽

Time Range ◽

Ecological Research ◽

Data Accessibility ◽

Web Based ◽

South Tyrol ◽

Research Site ◽

User Friendly

Easily accessible data is an essential requirement for scientific data analysis. The Data Browser Matsch | Mazia was designed to provide a fast and comprehensible solution to access, visualize and download the microclimatic measurements of the IT 25 LT(S)ER Match | Mazia research site in South Tyrol, Northern Italy, with the overall aim to provide straightforward data accessibility and enhance dissemination. Data Browser Matsch | Mazia is a user-friendly web-based application to visualize and download micrometeorological and biophysical time series of the Long-Term Socio-Ecological Research site Matsch | Mazia in South Tyrol, Italy. It is designed both for the general public and researchers. The Data Browser Matsch | Mazia drop-down menus allow the user to query the InfluxDB database in the backend by selecting the measurements, time range, land use and elevation. Interactive Grafana dashboards show dynamic graphs of the time series.

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Pengembangan Sistem Informasi Industri Jasa Menjahit Online Berbasis Web Menggunakan Metode Waterfall

JISKA (Jurnal Informatika Sunan Kalijaga) ◽

10.14421/jiska.2020.52-06 ◽

2020 ◽

Vol 5 (2) ◽

pp. 116

Author(s):

Elsa Oktavia ◽

Yulindon Yulindon ◽

Rahmat Hidayat

Keyword(s):

Information Systems ◽

Web Application ◽

Large Scale ◽

Design Work ◽

Financial Reports ◽

Web Based ◽

Work Systems ◽

Face To Face ◽

Service Information ◽

Drastic Increase

Information systems are currently increasing very rapidly, but it is unfortunate if the utilization is not yet optimal. Reviewing the data from literature studies and observations that have been made, many people need sewing services. The drastic increase in demand makes competition in the convection industry. Most of the work systems in the convection industry are done manually and are not economical. Product development also lacks creativity. Therefore, this researcher will use IT as marketing and design work, this can make processing time shorter and more optimal. Thus, customers will be facilitated in ordering ready-made clothes or clothes that match the customer's wishes by using a web application that only sends data on the size of the clothes or clothing model that the customer wants. This web-based application system can make it easier for customers to transact with the owner and transactions do not have to meet face to face. In addition, clothing sales and large-scale orders can be neatly organized and financial reports can be well structured and organized clearly. The results of this research will be in the form of research reports and web-based online sewing service information systems using the waterfall method.

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HeartBioPortal: an internet-of-omics for human cardiovascular disease data

10.1101/487744 ◽

2018 ◽

Author(s):

Bohdan Khomtchouk ◽

Kasra A Vand ◽

William C Koehler ◽

Diem-Trang Tran ◽

Kai Middlebrook ◽

...

Keyword(s):

Cardiovascular Disease ◽

Web Application ◽

Large Scale ◽

Data Science ◽

Cancer Genomics ◽

Clinical Information ◽

Visual Access ◽

Public Resources ◽

User Friendly ◽

Computational Platform

Cardiovascular disease (CVD) is the leading cause of death worldwide, causing over 17M deaths per year, which outpaces global cancer mortality rates. Despite these sobering statistics, the state-of-the-art in computational infrastructure to study datasets associated with CVD has lagged far behind public resources widely available in the oncology field, where improved data science and visualization methods have led to the development of large-scale cancer genomics resources like MSKCC's cBioPortal or NCI's Genomic Data Commons (GDC) Portal. Developing a similar user-friendly computational platform could significantly lower the barriers between complex CVD data and researchers who want rapid, intuitive, and high-quality visual access to molecular profiles and clinical attributes from existing CVD projects. Here we present HeartBioPortal: a publicly available web application that provides intuitive visualization, analysis, and downloads of large-scale CVD data currently focused on gene expression, genetic association, and ancestry information. By democratizing access to anonymized CVD data, HeartBioPortal's aim is to integrate relevant omics and clinical information across the biological dataverse to support CVD clinicians and researchers.

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RaDMaX online: a web-based program for the determination of strain and damage profiles in irradiated crystals using X-ray diffraction

Journal of Applied Crystallography ◽

10.1107/s1600576720002514 ◽

2020 ◽

Vol 53 (2) ◽

pp. 587-593

Author(s):

A. Boulle ◽

V. Mergnac

Keyword(s):

Web Application ◽

The Internet ◽

Programming Environment ◽

X Ray Diffraction ◽

Web Browser ◽

Web Based ◽

X Ray ◽

Depth Profiles ◽

User Friendly

RaDMaX online is a major update to the previously published RaDMaX (radiation damage in materials analysed with X-ray diffraction) software [Souilah, Boulle & Debelle (2016). J. Appl. Cryst. 49, 311–316]. This program features a user-friendly interface that allows retrieval of strain and disorder depth profiles in irradiated crystals from the simulation of X-ray diffraction data recorded in symmetrical θ/2θ mode. As compared with its predecessor, RaDMaX online has been entirely rewritten in order to be able to run within a simple web browser, therefore avoiding the necessity to install any programming environment on the users' computers. The RaDMaX online web application is written in Python and developed within a Jupyter notebook implementing graphical widgets and interactive plots. RaDMaX online is free and open source and can be accessed on the internet at https://aboulle.github.io/RaDMaX-online/.

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