scholarly journals The COMBAT-TB Workbench: Making powerful M. tuberculosis bioinformatics accessible

2021 ◽  
Author(s):  
Peter van Heusden ◽  
Ziphozahe Mashologu ◽  
Thoba Lose ◽  
Robin Warren ◽  
Alan Christoffels
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Software Components ◽  
Web Interface ◽  
Sample Analysis ◽  
Web Based ◽  
Workflow Execution ◽  
The Galaxy ◽  
User Friendly ◽  
Management Capabilities ◽  
Bioinformatics Workflow

Whole Genome Sequencing (WGS) is a powerful method for detecting drug resistance, genetic diversity and transmission dynamics of Mycobacterium tuberculosis. Implementation of WGS in public health microbiology laboratories is impeded by a lack of user-friendly, automated and semi-automated pipelines. We present the COMBAT-TB workbench, a modular, easy to install application that provides a web based environment for Mycobacterium tuberculosis bioinformatics. The COMBAT-TB Workbench is built using two main software components: the IRIDA Platform for its web-based user interface and data management capabilities and the Galaxy bioinformatics workflow platform for workflow execution. These components are combined into a single easy to install application using Docker container technology. We implemented two workflows, for M. tuberculosis sample analysis and phylogeny, in Galaxy. Building our workflows involved updating some Galaxy tools (Trimmomatic, snippy and snp-sites) and writing new Galaxy tools (snp-dists, TB-Profiler, tb_variant_filter and TB Variant Report). The irida-wf-ga2xml tool was updated to be able to work with recent versions of Galaxy and was further developed into IRIDA plugins for both workflows. In the case of the M. tuberculosis sample analysis an interface was added to update the metadata stored for each sequence sample with results gleaned from the Galaxy workflow output. Data can be loaded into the COMBAT-TB Workbench via the web interface or via the command line IRIDA uploader tool. The COMBAT-TB Workbench application deploys IRIDA, the COMBAT-TB IRIDA plugins, the MariaDB database and Galaxy using Docker containers (https://github.com/COMBAT-TB/irida-galaxy-deploy).

scholarly journals A repository of web-based bioinformatics resources developed in India

2020 ◽  
Author(s):  
Abhishek Agarwal ◽  
Piyush Agrawal ◽  
Aditi Sharma ◽  
Vinod Kumar ◽  
Chirag Mugdal ◽  
...  
Keyword(s):  
Scientific Community ◽  
Biological Databases ◽  
Web Interface ◽  
Web Based ◽  
Link Type ◽  
Complete Detail ◽  
User Friendly

AbstractIndiaBioDb (https://webs.iiitd.edu.in/raghava/indiabiodb/) is a manually curated comprehensive repository of bioinformatics resources developed and maintained by Indian researchers. This repository maintains information about 543 freely accessible functional resources that include around 258 biological databases. Each entry provides a complete detail about a resource that includes the name of resources, web link, detail of publication, information about the corresponding author, name of institute, type of resource. A user-friendly searching module has been integrated, which allows users to search our repository on any field. In order to retrieve categorized information, we integrate the browsing facility in this repository. This database can be utilized for extracting the useful information regarding the present scenario of bioinformatics inclusive of all research labs funded by government and private bodies of India. In addition to web interface, we also developed mobile to facilitate the scientific community.

AUTOMATIC PORTAL GENERATION BASED ON WORKFLOW DESCRIPTION

2011 ◽  
Vol 21 (02) ◽  
pp. 155-171
Author(s):  
CORAL WALKER ◽  
DASHAN LU ◽  
DAVID W. WALKER
Keyword(s):  
Visual Programming ◽  
Programming Environment ◽  
Distributed Environment ◽  
Service Oriented Architectures ◽  
Web Based ◽  
Workflow Execution ◽  
Execution Engine ◽  
Problem Solving Environment ◽  
Service Oriented ◽  
User Friendly

Distributed scientific and engineering computations on service-oriented architectures are often represented as data-driven workflows. Workflows are a convenient abstraction that allows users to compose applications in a visual programming environment, and execute them by means of a workflow execution engine. For a large class of scientific applications web-based portals can provide a user-friendly problem-solving environment that hides the complexities of executing workflow applications in a distributed environment. However, the creation and configuration of an application portal requires considerable expertise in portal technologies, which scientific end-users generally do not have. To address this problem this paper presents tools for automatically converting a workflow into a fully configured portal which can then be used to execute the workflow.

scholarly journals Tribe: The collaborative platform for reproducible web-based analysis of gene sets

2016 ◽  
Author(s):  
René A. Zelaya ◽  
Aaron K. Wong ◽  
Alex T. Frase ◽  
Marylyn D. Ritchie ◽  
Casey S. Greene
Keyword(s):  
Open Source ◽  
Web Interface ◽  
Web Based ◽  
Gene Set ◽  
Collaborative Editing ◽  
Gene Sets ◽  
Collaborative Platform ◽  
Set Up ◽  
User Friendly ◽  
Multi Server

AbstractBackgroundThe adoption of new bioinformatics webservers provides biological researchers with new analytical opportunities but also raises workflow challenges. These challenges include sharing collections of genes with collaborators, translating gene identifiers to the most appropriate nomenclature for each server, tracking these collections across multiple analysis tools and webservers, and maintaining effective records of the genes used in each analysis.DescriptionIn this paper, we present the Tribe webserver (available at https://tribe.greenelab.com), which addresses these challenges in order to make multi-server workflows seamless and reproducible. This allows users to create analysis pipelines that use their own sets of genes in combinations of specialized data mining webservers and tools while seamlessly maintaining gene set version control. Tribe’s web interface facilitates collaborative editing: users can share with collaborators, who can then view, download, and edit these collections. Tribe’s fully-featured API allows users to interact with Tribe programmatically if desired. Tribe implements the OAuth 2.0 standard as well as gene identifier mapping, which facilitates its integration into existing servers. Access to Tribe’s resources is facilitated by an easy-to-install Python application called tribe-client. We provide Tribe and tribe-client under a permissive open-source license to encourage others to download the source code and set up a local instance or to extend its capabilities.ConclusionsThe Tribe webserver addresses challenges that have made reproducible multi-webserver workflows difficult to implement until now. It is open source, has a user-friendly web interface, and provides a means for researchers to perform reproducible gene set based analyses seamlessly across webservers and command line tools.

scholarly journals EWAS-Galaxy: a tools suite for population epigenetics integrated into Galaxy

2019 ◽  
Author(s):  
Katarzyna Murat ◽  
Björn Grüning ◽  
Paulina Wiktoria Poterlowicz ◽  
Gillian Westgate ◽  
Desmond J Tobin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Association Studies ◽  
Web Based ◽  
Genome Wide ◽  
Methylation Assay ◽  
The Galaxy ◽  
Common Technique ◽  
Analyse Data ◽  
User Friendly ◽  
Dna Methylation Analysis

AbstractBackgroundEpigenome-wide association studies (EWAS) analyse genome-wide activity of epigenetic marks in cohorts of different individuals to find associations between epigenetic variation and phenotype. One of the most common technique used in EWAS studies is the Infinium Methylation Assay, which quantifies the DNA methylation level of over 450k loci. Although a number of bioinformatics tools have been developed to analyse the assay they require some programming skills and experience to use them.ResultsWe have developed a collection of user-friendly tools for the Galaxy platform for those without experience aimed at DNA methylation analysis using the Infinium Methylation Assay. Our tool suite is integrated into Galaxy (http://galaxyproject.org), web based platform. This allows users to analyse data from the Infinium Methylation Assay in the easiest possible way.ConclusionsThe EWAS suite provides a group of integrated tools that combine analytical methods into a range of handy analysis pipelines. Our tool suite is available from the Galaxy test toolshed, GitHub repository and also as a Docker image. The aim of this project is to make EWAS analysis more flexible and accessible to everyone.

scholarly journals PharmaKU: A Web-Based Tool Aimed at Improving Outreach and Clinical Utility of Pharmacogenomics

2021 ◽  
Vol 11 (3) ◽  
pp. 210
Author(s):  
Sumi Elsa John ◽  
Arshad Mohamed Channanath ◽  
Prashantha Hebbar ◽  
Rasheeba Nizam ◽  
Thangavel Alphonse Thanaraj ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Clinical Utility ◽  
Reference Genome ◽  
Web Interface ◽  
Sequencing Technology ◽  
Web Based ◽  
Related Information ◽  
Clinical Reality ◽  
Reference Genome Assembly ◽  
User Friendly

With the tremendous advancements in genome sequencing technology in the field of pharmacogenomics, data have to be made accessible to be more efficiently utilized by broader clinical disciplines. Physicians who require the drug–genome interactome information, have been challenged by the complicated pharmacogenomic star-based classification system. We present here an end-to-end web-based pharmacogenomics tool, PharmaKU, which has a comprehensive interface easy-to-use interface. PharmaKU can help to overcome several hurdles posed by previous pharmacogenomics tools, including input in hg38 format only, while hg19/GRCh37 is now the most popular reference genome assembly among clinicians and geneticists, as well as the lack of clinical recommendations and other pertinent dosage-related information. This tool extracts genetic variants from nine well-annotated pharmacogenes (for which diplotype to phenotype information is available) from whole genome variant files and uses Stargazer software to assign diplotypes and apply prescribing recommendations from pharmacogenomic resources. The tool is wrapped with a user-friendly web interface, which allows for choosing hg19 or hg38 as the reference genome version and reports results as a comprehensive PDF document. PharmaKU is anticipated to enable bench to bedside implementation of pharmacogenomics knowledge by bringing precision medicine closer to a clinical reality.

scholarly journals Prediction of the Remaining Useful Life of Aircraft Systems via Web Interface

2020 ◽  
Vol 16 (04) ◽  
pp. 23
Author(s):  
Daniel Azevedo ◽  
Bernardete Ribeiro ◽  
Alberto Cardoso
Keyword(s):  
Machine Learning ◽  
Health Management ◽  
Remaining Useful Life ◽  
Machine Learning Techniques ◽  
Web Interface ◽  
Web Based ◽  
Aircraft Systems ◽  
Public Data ◽  
Useful Life ◽  
User Friendly

In this work a web-based tool is presented for the simulation of a Prognostics and Health Management (PHM) system used for exploring and testing different machine learning experimental scenarios with the goal of predicting the Remaining Useful Life (RUL) of aircraft systems. With this tool, the user can select a set of options like the datasets to use, its size, the machine learning method to apply for the RUL prediction and the metrics used for comparing the results. The proposed datasets correspond to public data extracted from a model which aims to simulate a Turbofan Engine dataset of an aircraft. Also, three different State of the Art machine learning techniques are made available to be applied and tested: a Similarity-based, a Neural Network-based and an Extrapolation-based approach. The results obtained by the different approaches can be graphically compared in the web interface. As the methods are executed remotely, the user incurs no computational costs, which constitutes an advantage of using this tool. This web tool aims to be a user-friendly interface used for simulating online experiments regarding the RUL prediction.

Design and Implementation of a Mobile and Portable Lifelog Media System

2010 ◽  
pp. 718-729
Author(s):  
Baud Haryo Prananto
Keyword(s):  
Management System ◽  
Wearable Devices ◽  
Multimedia Data ◽  
Web Interface ◽  
User Friendliness ◽  
Web Based ◽  
Design And Implementation ◽  
Media System ◽  
Everyday Experiences ◽  
User Friendly

Lifelog media system stores and manages users’ everyday experiences in the form of multimedia data. To build such a system, we require an integrated framework for capturing the experiences to multimedia data, storing and managing those data, and also presenting the data to the user in a user-friendly way. Due to the mobility of the user, we built a mobile framework that includes wearable devices that enable the user to capture experiences easily, and a Web-based management system that can be presented anytime and anywhere using Web interface. In this chapter, we provide solutions for some issues that emerge in this system (such as mobility and user friendliness), mostly on the database performance.

scholarly journals EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening

2020 ◽  
Vol 36 (14) ◽  
pp. 4200-4202 ◽  
Author(s):  
Douglas E V Pires ◽  
Wandré N P Veloso ◽  
YooChan Myung ◽  
Carlos H M Rodrigues ◽  
Michael Silk ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Web Interface ◽  
Web Based ◽  
Protein Target ◽  
User Friendly ◽  
Library Selection ◽  
Intuitive Interface

Abstract Summary EasyVS is a web-based platform built to simplify molecule library selection and virtual screening. With an intuitive interface, the tool allows users to go from selecting a protein target with a known structure and tailoring a purchasable molecule library to performing and visualizing docking in a few clicks. Our system also allows users to filter screening libraries based on molecule properties, cluster molecules by similarity and personalize docking parameters. Availability and implementation EasyVS is freely available as an easy-to-use web interface at http://biosig.unimelb.edu.au/easyvs. Contact [email protected] or [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A bioinformatics WGS workflow for clinical Mycobacterium tuberculosis complex isolate analysis, validated using a reference collection extensively characterized with conventional methods and in silico approaches

2021 ◽  
Author(s):  
Bert Bogaerts ◽  
Thomas Delcourt ◽  
Karine Soetaert ◽  
Samira Boarbi ◽  
Pieter-Jan Ceyssens ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
In Silico ◽  
High Performance ◽  
Performance Metrics ◽  
Complete Characterization ◽  
Non Profit ◽  
Public Data ◽  
The Galaxy ◽  
Phenotypic Methods ◽  
Bioinformatics Workflow

The use of whole genome sequencing (WGS) for routine typing of bacterial isolates has increased substantially in recent years. For Mycobacterium tuberculosis (MTB), in particular, WGS has the benefit of drastically reducing the time to generate results compared to most conventional phenotypic methods. Consequently, a multitude of solutions for analyzing WGS MTB data have been developed, but their successful integration in clinical and national reference laboratories is hindered by the requirement for their validation, for which a consensus framework is still largely absent. We developed a bioinformatics workflow for (Illumina) WGS-based routine typing of MTB Complex (MTBC) member isolates allowing complete characterization including (sub)species confirmation and identification (16S, csb/RD, hsp65), Single Nucleotide Polymorphism (SNP)-based antimicrobial resistance (AMR) prediction, and pathogen typing (spoligotyping, SNP barcoding, and core genome MultiLocus Sequence Typing). Workflow performance was validated on a per-assay basis using a collection of 238 in-house sequenced MTBC isolates, extensively characterized with conventional molecular biology-based approaches supplemented with public data. For SNP-based AMR prediction, results from molecular genotyping methods were supplemented with in silico modified datasets allowing to greatly increase the set of evaluated mutations. The workflow demonstrated very high performance with performance metrics >99% for all assays, except for spoligotyping where sensitivity dropped to ∼90%. The validation framework for our WGS-based bioinformatics workflow can aid standardization of bioinformatics tools by the MTB community and other SNP-based applications regardless of the targeted pathogen(s). The bioinformatics workflow is available for academic and non-profit usage through the Galaxy instance of our institute at https://galaxy.sciensano.be.

The Role of Web Based Accounting Online System 2.0 as the Company's Income and Expense Management

2017 ◽  
Vol 1 (1) ◽  
pp. 44-49
Author(s):  
Nur Azizah ◽  
Dedeh Supriyanti ◽  
Siti Fairuz Aminah Mustapha ◽  
Holly Yang
Keyword(s):  
Financial Management ◽  
Accounting System ◽  
Bank Account ◽  
Web Based ◽  
Online System ◽  
Version 2.0 ◽  
User Friendly ◽  
The Impact ◽  
A Company

In a company, the process of income and expense of money must have a profit-generating goal base. The success of financial management within the company, can be monitored from the ability of the financial management in managing the finances and utilize all the opportunities that exist with as much as possible with the aim to control the company's cash (cash flow) and the impact of generating profits in accordance with expectations. With a web-based online accounting system version 2.0, companies can be given the ease to manage money in and out of the company's cash. It has a user friendly system with navigation that makes it easy for the financial management to use it. Starting from the creation of a company's cash account used as a cash account and corporate bank account on the system, deletion or filing of cash accounts, up to the transfer invoice creation feature, receive and send money. Thus, this system is very effective and efficient in the management of income and corporate cash disbursements.   Keywords:​Accounting Online System, Financial Management, Cash and Bank

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