scholarly journals Primer Server - A web application to design primers for the amplification of unique DNA targets in complex genomes

2018 ◽  
Author(s):  
Takao Shibamoto ◽  
Kokulapalan Wimalanathan ◽  
Erica Unger-Wallace ◽  
Erik Vollbrecht
Keyword(s):  
Web Application ◽  
Genetic Material ◽  
Pcr Primers ◽  
Test Tube ◽  
Dna Bases ◽  
Web Based ◽  
User Input ◽  
Server Side ◽  
Target Binding ◽  
User Friendly

Polymerase Chain Reaction (PCR) is one of the most important inventions of the 20th century in molecular biology. PCR is a technique to amplify or make in a test tube many copies of a specific DNA region. Miniscule amounts of the genetic material from any organism can now be amplified to identify individuals, manipulate DNA, detect infectious organisms including the viruses that cause AIDS, hepatitis, and tuberculosis, detect genetic variations including mutations in genes, and numerous other tasks. PCR primers are short, single-stranded DNAs that define the section of DNA to be amplified. Two primers are used in each PCR reaction, designed so that they bind at flanking locations surrounding the target region. Critically, off-target binding may lead to experimental failure or worse, to misleading results. Thus, potential primers of approximately 20 DNA bases in length, must be examined for off-target binding among, for example, the 3.2 billion DNA bases from all human chromosomes, the human genome. The purpose of our study is to make a user-friendly tool (Primer Server) that can design PCR primers efficiently and accurately as well as visualize the designed primers. Our web-based bioinformatics tool selects optimal primer sequences within the starting material by using a C module called primer3 and then prioritizing and/or eliminating potential primers based on comparison of the primer bases against all bases in the genome using an algorithm  called BLAST. This tool has an easy-to-use interface which was designed using Angular2, and an efficient server-side code written in Python. While similar tools exist, our tool is more user-friendly, efficient and uses extensive form validation to minimize errors in the user input. Our tool can be used to design primers that will be used in laboratory experiments to amplify DNA from various organisms, including large, complex genomes such as humans, other animals and plants.

scholarly journals amica: an interactive and user-friendly web-platform for the analysis of proteomics data

2021 ◽  
Author(s):  
Sebastian Didusch ◽  
Moritz Madern ◽  
Markus Hartl ◽  
Manuela Baccarini
Keyword(s):  
Quantitative Proteomics ◽  
Web Application ◽  
Biological Network ◽  
Life Sciences ◽  
Proteomics Data ◽  
Web Based ◽  
User Input ◽  
User Friendly ◽  
Different Sources ◽  
Web Platform

Quantitative proteomics has become an increasingly prominent tool in the study of life sciences. A substantial hurdle for many biologists are, however, the intricacies involved in the associated high troughput data analysis. In order to facilitate this task for users with little background knowledge in proteomics, we have developed amica, a freely available open-source web-based software that accepts proteomic input files from different sources and provides quality control, differential expression, biological network and over-representation analysis on the basis of minimal user input. Scientists can use amica interactively to compare proteins across multiple groups, create customized output graphics, and ultimately export the results in a tab-separated format that can be shared with collaborators. Availability and Implementation: The code for the application, input data and documentation can be accessed online at https://github.com/tbaccata/amica and is also incorporated in the web application. A freely available version of amica is available at https://bioapps.maxperutzlabs.ac.at/app/amica.

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.  

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

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.

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

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.

scholarly journals Prosedur efektif pengembangan aplikasi basis data

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Zulkarnaen Hatala
Keyword(s):  
Web Application ◽  
Specific Requirement ◽  
Application System ◽  
Web Based ◽  
Database Application ◽  
Server Side ◽  
The Right ◽  
Client Side ◽  
The Web

Abstract—Efficient and quick procedure to build a web application is presented. The steps are intended to build a database application system with hundreds of tables. The procedure can minimize tasks needed to write code and doing manual programming line by line. The intention also to build rapidly web-based database application. In this method security concerning authentification and authorization already built in ensuring the right and eligible access of the user to the system. The end result is ready to use the web-based 3-tier application. Moreover, the application is still flexible to be customized and to be enhanced to suit more specific requirement in part of each module of the software both the server-side and client-side programming codes. Abstrak—Pada penelitian kali ini diusulkan prosedur cepat dan efisien pengembangan aplikasi basis data menggunakan generator aplikasi. Bertujuan untuk meminimalisir penulisan bahasa pemograman. Keuntungan dari prosedur ini adalah bisa digunakan untuk mengembangkan aplikasi basis data secara cepat terutama dengan sistem basis data yang terdiri dari banyak tabel. Hak akses dan prosedur keamanan standar telah disediakan sehingga setiap user terjamin haknya terhadap entitas tertentu di basis data. Hasil generasi adalah aplikasi basis data berbasis web yang siap pakai. Sistem aplikasi yang terbentuk masih sangat lentur untuk untuk dilakukan penyesuaian setiap komponen aplikasi baik di sisi server maupun di sisi client.

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

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/.

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

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.  

Software Architectures and Requirements for a Web-Based Survey System

2011 ◽  
pp. 87-109
Author(s):  
Dirk Baldwin ◽  
Suresh Chalasani
Keyword(s):  
Web Application ◽  
Application Server ◽  
Web Based ◽  
Server Side ◽  
Business Partners ◽  
University Of Wisconsin ◽  
Survey System ◽  
Survey Responses ◽  
The University ◽  
The Web

Many businesses obtain feedback by surveying customers and business partners. Increasingly, these surveys are conducted via the Web. This chapter reviews briefly literature regarding Web-based surveys and describes a software architecture for a Web-based survey system. The architecture for the survey system is based on three-tiers comprised of a Web server, Web application server, and database server. The Web application server hosts the application modules that display and process the surveys. The application software consists of packages for establishing connections to the database and for reading static and dynamic data from the database. The processed surveys are written to the database with the survey responses. This system allows for anonymous survey responses and maintains user confidentiality. At the University of Wisconsin-Parkside, we have implemented this Web-based survey system, and used it to conduct three different surveys. This survey system is easily extensible to new surveys, and is used for instructional purposes to teach server-side programming. In this chapter, we discuss the key ideas behind the design and implementation of the extensible survey system, and provide results on its application.

scholarly journals G4Hunter web application: a web server for G-quadruplex prediction

2019 ◽  
Vol 35 (18) ◽  
pp. 3493-3495 ◽  
Author(s):  
Václav Brázda ◽  
Jan Kolomazník ◽  
Jiří Lýsek ◽  
Martin Bartas ◽  
Miroslav Fojta ◽  
...  
Keyword(s):  
Data Storage ◽  
Web Application ◽  
Data Representation ◽  
Complete Characterization ◽  
Supplementary Information ◽  
Web Based ◽  
Rna Molecules ◽  
Dna And Rna ◽  
Sorting Data ◽  
User Friendly

Abstract Motivation Expanding research highlights the importance of guanine quadruplex structures. Therefore, easy-accessible tools for quadruplex analyses in DNA and RNA molecules are important for the scientific community. Results We developed a web version of the G4Hunter application. This new web-based server is a platform-independent and user-friendly application for quadruplex analyses. It allows retrieval of gene/nucleotide sequence entries from NCBI databases and provides complete characterization of localization and quadruplex propensity of quadruplex-forming sequences. The G4Hunter web application includes an interactive graphical data representation with many useful options including visualization, sorting, data storage and export. Availability and implementation G4Hunter web application can be accessed at: http://bioinformatics.ibp.cz. Supplementary information Supplementary data are available at Bioinformatics online.

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