scholarly journals CRAMER: a lightweight, highly customizable web-based genome browser supporting multiple visualization instances

2020 ◽  
Vol 36 (11) ◽  
pp. 3556-3557
Author(s):  
M Anastasiadi ◽  
E Bragin ◽  
P Biojoux ◽  
A Ahamed ◽  
J Burgin ◽  
...  
Keyword(s):  
Web Application ◽  
Variant Calling ◽  
Genomic Data ◽  
Genome Browser ◽  
Supplementary Information ◽  
Web Based ◽  
Server Side ◽  
Genome Browsers ◽  
Set Up ◽  
Effective Visualization

Abstract Summary In recent years, the ability to generate genomic data has increased dramatically along with the demand for easily personalized and customizable genome browsers for effective visualization of diverse types of data. Despite the large number of web-based genome browsers available nowadays, none of the existing tools provides means for creating multiple visualization instances without manual set up on the deployment server side. The Cranfield Genome Browser (CRAMER) is an open-source, lightweight and highly customizable web application for interactive visualization of genomic data. Once deployed, CRAMER supports seamless creation of multiple visualization instances in parallel while allowing users to control and customize multiple tracks. The application is deployed on a Node.js server and is supported by a MongoDB database which stored all customizations made by the users allowing quick navigation between instances. Currently, the browser supports visualizing a large number of file formats for genome annotation, variant calling, reads coverage and gene expression. Additionally, the browser supports direct Javascript coding for personalized tracks, providing a whole new level of customization both functionally and visually. Tracks can be added via direct file upload or processed in real-time via links to files stored remotely on an FTP repository. Furthermore, additional tracks can be added by users via simple drag and drop to an existing visualization instance. Availability and implementation CRAMER is implemented in JavaScript and is publicly available on GitHub on https://github.com/FadyMohareb/cramer. The application is released under an MIT licence and can be deployed on any server running Linux or Mac OS. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals BioViz Connect: Web application linking CyVerse science gateway resources to genomic visualization in the Integrated Genome Browser

2020 ◽  
Author(s):  
Nowlan H Freese ◽  
Karthik Raveendran ◽  
Chaitanya Kintali ◽  
Srishti Tiwari ◽  
Pawan Bole ◽  
...  
Keyword(s):  
Visual Analytics ◽  
Web Application ◽  
Visual Analysis ◽  
Genomic Data ◽  
Application Programming Interface ◽  
Genome Browser ◽  
Rna Seq ◽  
Web Based ◽  
Science Gateways ◽  
Application Programming

AbstractBackgroundVisualization of genomic data is a key step in validating methods and results. Web-based science gateways such as CyVerse provide storage and analysis tools for genomic data but often lack visualization capability. Desktop visualization tools like Integrated Genome Browser (IGB) enable highly interactive data visualization but are difficult to deploy in science gateways. Developing ways for gateways to interoperate with pre-existing external tools like IGB would enhance their value to users.ResultsWe developed BioViz Connect, a new web application that connects CyVerse and IGB using the CyVerse Terrain Application Programming Interface (API). Using BioViz Connect, users can (i) stream their CyVerse data to IGB for visualization, (ii) add IGB specific metadata such as genome version and track appearance to CyVerse data, and (iii) run compute-intensive visual analytics functions to create new visualizations for IGB. To demonstrate BioViz Connect, we present an example visual analysis of RNA-Seq data from Arabidopsis thaliana plants undergoing heat and desiccation stresses. The example shows how researchers can seamlessly analyze and visualize their CyVerse data in IGB. BioViz Connect is accessible from https://bioviz.org.ConclusionsBioViz Connect demonstrates a new way to integrate science gateways with desktop applications using APIs.

scholarly journals TGAC Browser: An open-source genome browser for non-model organisms

2019 ◽  
Author(s):  
Anil S. Thanki ◽  
Xingdong Bian ◽  
Robert P. Davey
Keyword(s):  
Open Source ◽  
Genomic Data ◽  
Vital Role ◽  
Genome Browser ◽  
Model Organisms ◽  
Genome Browsers ◽  
Public Repositories ◽  
Set Up ◽  
User Friendly ◽  
Ngs Data

Genome browsers play a vital role to provide visualisation for genomic data. It is often the case that bespoke genome browser customisations are required between different research groups, with an obvious necessity to update, upgrade and tailor tracks and features on a potentially frequent basis. However, most of the current genome browsers require highly curated data held in public repositories. Besides, these genome browsers often rely on particular dependencies, where writing plug-in or modifying existing code can be troublesome and resource expensive.We present TGAC Browser, a new open-source web-based genome browser designed to overcome shortcomings in available approaches. It uses a locally installed Ensembl Core Database schema and is also able to visualise data from well-known NGS data formats. We also added simple analysis functionality to perform BLAST searches within TGAC Browser. TGAC Browser also allows uploading your genomic data. TGAC Browser is an open-source, easy to set up, and user-friendly genome browser with minimal, lightweight configuration details.

scholarly journals PBrowse: A web-based platform for real-time collaborative exploration of genomic data

2016 ◽  
Author(s):  
Peter S. Szot ◽  
Andrian Yang ◽  
Xin Wang ◽  
Uwe Röhm ◽  
Koon Ho Wong ◽  
...  
Keyword(s):  
Real Time ◽  
Genomic Data ◽  
File Sharing ◽  
Genome Browser ◽  
Human Interaction ◽  
Supplementary Information ◽  
Web Based ◽  
Link Type ◽  
Multiple Users ◽  
Wide Range

ABSTRACTSummaryThe central task of a genome browser is to enable easy visual exploration of large genomic data to gain biological insight. Most existing genome browsers were designed for data exploration by individual users, while a few allow some limited forms of collaboration among multiple users, such as file sharing and wiki-style collaborative editing of gene annotations. Our work’s premise is that allowing sharing of genome browser views instantaneously in real-time enables the exchange of ideas and insight in a collaborative project, thus harnessing the wisdom of the crowd. PBrowse is a parallel-access real-time collaborative web-based genome browser that provides both an integrated, real-time collaborative platform and a comprehensive file sharing system. PBrowse also allows real-time track comment and has integrated group chat to facilitate interactive discussion among multiple users. Through the Distributed Annotation Server protocol, PBrowse can easily access a wide range of publicly available genomic data, such as the ENCODE data sets. We argue that PBrowse, with the re-designed user management, data management and novel collaborative layer based on Biodalliance, represents a paradigm shift from seeing genome browser merely as a tool of data visualisation to a tool that enables real-time human-human interaction and knowledge exchange in a collaborative setting.AvailabilityPBrowse is available at http://pbrowse.victorchang.edu.au, and its source code is available via the open source BSD 3 license at http://github.com/VCCRI/[email protected] InformationSupplementary video demonstrating collaborative feature of pbrowse is available in https://www.youtube.com/watch?v=ROvKXZoXiIc.

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 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.

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.

scholarly journals LogoJS: a Javascript package for creating sequence logos and embedding them in web applications

2020 ◽  
Vol 36 (11) ◽  
pp. 3573-3575
Author(s):  
Henry Pratt ◽  
Zhiping Weng
Keyword(s):  
Web Application ◽  
Web Applications ◽  
Supplementary Information ◽  
Computational Techniques ◽  
Web Based ◽  
Consensus Sequences ◽  
Graphic Sequence ◽  
Energy Penalty ◽  
Sequence Logos ◽  
Covalent Modifications

Abstract Summary Sequence logos were introduced nearly 30 years ago as a human-readable format for representing consensus sequences, and they remain widely used. As new experimental and computational techniques have developed, logos have been extended: extra symbols represent covalent modifications to nucleotides, logos with multiple letters at each position illustrate models with multi-nucleotide features and symbols extending below the x-axis may represent a binding energy penalty for a residue or a negative weight output from a neural network. Web-based visualization tools for genomic data are increasingly taking advantage of modern web technology to offer dynamic, interactive figures to users, but support for sequence logos remains limited. Here, we present LogoJS, a Javascript package for rendering customizable, interactive, vector-graphic sequence logos and embedding them in web applications. LogoJS supports all the aforementioned logo extensions and is bundled with a companion web application for creating and sharing logos. Availability and implementation LogoJS is implemented both in plain Javascript and ReactJS, a popular user-interface framework. The web application is hosted at logojs.wenglab.org. All major browsers and operating systems are supported. The package and application are open-source; code is available at GitHub. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

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.

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