scholarly journals WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Martin Lyčka ◽  
Vratislav Peska ◽  
Martin Demko ◽  
Ioannis Spyroglou ◽  
Agata Kilar ◽  
...  
Keyword(s):  
Restriction Fragment ◽  
Genome Stability ◽  
Tandem Repeats ◽  
Statistical Evaluation ◽  
Molecular Complexes ◽  
Web Based ◽  
Link Type ◽  
Precise Tool ◽  
User Friendly ◽  
Ngs Data

Abstract Background Telomeres, nucleoprotein structures comprising short tandem repeats and delimiting the ends of linear eukaryotic chromosomes, play an important role in the maintenance of genome stability. Therefore, the determination of the length of telomeres is of high importance for many studies. Over the last years, new methods for the analysis of the length of telomeres have been developed, including those based on PCR or analysis of NGS data. Despite that, terminal restriction fragment (TRF) method remains the gold standard to this day. However, this method lacks universally accepted and precise tool capable to analyse and statistically evaluate TRF results. Results To standardize the processing of TRF results, we have developed WALTER, an online toolset allowing rapid, reproducible, and user-friendly analysis including statistical evaluation of the data. Given its web-based nature, it provides an easily accessible way to analyse TRF data without any need to install additional software. Conclusions WALTER represents a major upgrade from currently available tools for the image processing of TRF scans. This toolset enables a rapid, highly reproducible, and user-friendly evaluation of almost any TRF scan including in-house statistical evaluation of the data. WALTER platform together with user manual describing the evaluation of TRF scans in detail and presenting tips and troubleshooting, as well as test data to demo the software are available at https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus/rg51/tab?tabId=125#WALTER and the source code at https://github.com/mlyc93/WALTER.

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

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]

scholarly journals TACITuS: transcriptomic data collector, integrator, and selector on big data platform

2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Salvatore Alaimo ◽  
Antonio Di Maria ◽  
Dennis Shasha ◽  
Alfredo Ferro ◽  
Alfredo Pulvirenti
Keyword(s):  
High Throughput ◽  
Rna Seq ◽  
Web Based ◽  
Large Bandwidth ◽  
Specific Analysis ◽  
Galaxy Environment ◽  
Public Repositories ◽  
Microarray Datasets ◽  
User Friendly ◽  
Ngs Data

Abstract Background Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate data from such resources, because the data is stored in large files, requiring large bandwidth to download and special purpose data manipulation tools to extract subsets relevant for the specific analysis. Results TACITuS is a web-based system that supports rapid query access to high-throughput microarray and NGS repositories. The system is equipped with modules capable of managing large files, storing them in a cloud environment and extracting subsets of data in an easy and efficient way. The system also supports the ability to import data into Galaxy for further analysis. Conclusions TACITuS automates most of the pre-processing needed to analyze high-throughput microarray and NGS data from large publicly-available repositories. The system implements several modules to manage large files in an easy and efficient way. Furthermore, it is capable deal with Galaxy environment allowing users to analyze data through a user-friendly interface.

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.

scholarly journals PhageTerm: a Fast and User-friendly Software to Determine Bacteriophage Termini and Packaging Mode using randomly fragmented NGS data

2017 ◽  
Author(s):  
Julian Garneau ◽  
Florence Depardieu ◽  
Louis-Charles Fortier ◽  
David Bikard ◽  
Marc Monot
Keyword(s):  
High Throughput Sequencing ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Link Type ◽  
Sequencing Technologies ◽  
Statistical Framework ◽  
Fastq Format ◽  
Viral Particles ◽  
User Friendly ◽  
Ngs Data

ABSTRACTBacteriophages are the most abundant viruses on earth and display an impressive genetic as well as morphologic diversity. Among those, the most common order of phages is the Caudovirales, whose viral particles packages linear double stranded DNA (dsDNA). In this study we investigated how the information gathered by high throughput sequencing technologies can be used to determine the DNA termini and packaging mechanisms of dsDNA phages. The wet-lab procedures traditionally used for this purpose rely on the identification and cloning of restriction fragment which can be delicate and cumbersome. Here, we developed a theoretical and statistical framework to analyze DNA termini and phage packaging mechanisms using next-generation sequencing data. Our methods, implemented in the PhageTerm software, work with sequencing reads in fastq format and the corresponding assembled phage genome.PhageTerm was validated on a set of phages with well-established packaging mechanisms representative of the termini diversity: 5’cos (lambda), 3’cos (HK97), pac (P1), headful without a pac site (T4), DTR (T7) and host fragment (Mu). In addition, we determined the termini of 9Clostridium difficilephages and 6 phages whose sequences where retrieved from the sequence read archive (SRA).A direct graphical interface is available as a Galaxy wrapper version athttps://galaxy.pasteur.frand a standalone version is accessible athttps://sourceforge.net/projects/phageterm/.

scholarly journals neoANT-HILL: an integrated tool for identification of potential neoantigens

2019 ◽  
Author(s):  
Ana Carolina M F Coelho ◽  
André L Fonseca ◽  
Danilo L Martins ◽  
Lucas M da Cunha ◽  
Paulo B R Lins ◽  
...  
Keyword(s):  
Immune Responses ◽  
False Positive ◽  
Somatic Mutations ◽  
Cancer Genome ◽  
Current Work ◽  
Rna Seq ◽  
Link Type ◽  
Technological Advances ◽  
User Friendly ◽  
Ngs Data

AbstractCancer neoantigens have attracted great interest in immunotherapy due to their ability to elicit antitumoral immune responses. These antigens are formed due to somatic mutations in the cancer genome that result in alterations of the original protein. Although current technological advances in neoantigen identification, it remains a challenging and a large number of false-positive continue to exist. In the current work, we present neoANT-HILL, an automatized user-friendly tool that integrates several immunogenomic analysis to improve neoantigens detection from NGS data. The program input can be a file with somatic mutations called and/or RNA-seq data. Our tool was applied on somatic mutations of melanoma dataset from TCGA and found that neoANT-HILL was able to predicted potential neoantigens. The software is available on github athttps://github.com/neoanthill/neoANT-HILL.

scholarly journals OUTBREAK: a user-friendly georeferencing online tool for disease surveillance

2021 ◽  
Vol 54 (1) ◽  
Author(s):  
Raúl Arias-Carrasco ◽  
Jeevan Giddaluru ◽  
Lucas E. Cardozo ◽  
Felipe Martins ◽  
Vinicius Maracaja-Coutinho ◽  
...  
Keyword(s):  
Real Time ◽  
Disease Surveillance ◽  
Input Data ◽  
Policy Decisions ◽  
Web Tool ◽  
Web Based ◽  
Online Tool ◽  
Link Type ◽  
Health Authorities ◽  
User Friendly

AbstractThe current COVID-19 pandemic has already claimed more than 3.7 million victims and it will cause more deaths in the coming months. Tools that track the number and locations of cases are critical for surveillance and help in making policy decisions for controlling the outbreak. However, the current surveillance web-based dashboards run on proprietary platforms, which are often expensive and require specific computational knowledge. We developed a user-friendly web tool, named OUTBREAK, that facilitates epidemic surveillance by showing in an animated graph the timeline and geolocations of cases of an outbreak. It permits even non-specialist users to input data most conveniently and track outbreaks in real-time. We applied our tool to visualize the SARS 2003, MERS, and COVID19 epidemics, and provided them as examples on the website. Through the zoom feature, it is also possible to visualize cases at city and even neighborhood levels. We made the tool freely available at https://outbreak.sysbio.tools/. OUTBREAK has the potential to guide and help health authorities to intervene and minimize the effects of outbreaks.

scholarly journals figureComposer: A web-based interactive multi-panel bio-infographic designing tool

2020 ◽  
Author(s):  
Kejie Li ◽  
Jessica Hurt ◽  
Christopher D. Whelan ◽  
Ravi Challa ◽  
Dongdong Lin ◽  
...  
Keyword(s):  
High Resolution ◽  
Web Tool ◽  
Bioinformatics Tool ◽  
Web Based ◽  
Link Type ◽  
High Resolution Images ◽  
Fit For Purpose ◽  
Programming Skills ◽  
User Friendly ◽  
Publication Quality

AbstractBackgroundMany fit-for-purpose bioinformatics tools generate plots to investigate data quality and illustrate findings. However, assembling individual plots in different formats from various sources into one high-resolution figure requires mastery of commercial tools or even programming skills. In addition, it is a time-consuming and sometimes frustrating process even for scientists with modest computational skills.ResultsWe developed figureComposer, a web-based bioinformatics tool that interactively arranges high-resolution images in various formats, mainly SVG to produce one multi-panel publication-quality composite figure in both PDF and interactive HTML formats in a user-friendly matter, requiring no programming skills.ConclusionsfigureComposer is open-source and publicly available web tool that can be accessed online at https://baohongz.github.io/figureComposer while the source code is provided at https://github.com/baohongz/figureComposer.

scholarly journals GiraFFe Browse: A lightweight web based tool for inspecting GFF and FASTA data

2018 ◽  
Author(s):  
Owen Garland ◽  
Amanda Clare ◽  
Wayne Aubrey
Keyword(s):  
Escherichia Coli ◽  
Software Engineering ◽  
Open Source ◽  
Fasta File ◽  
Web Based ◽  
Link Type ◽  
European Nucleotide Archive ◽  
Specialist Knowledge ◽  
Engineering Practices ◽  
User Friendly

AbstractSummaryGiraFFe Browse is a tool aimed at making GFF and FASTA data more useful and accessible to researchers. Existing solutions are large in scope and difficult to maintain without specialist knowledge of computer systems. GiraFFe Browse is a lightweight alternative, built using modern software engineering practices with a focus on being developer and user friendly.Availability and implementationGiraFFe Browse is open source (GPL) software that is available from the Github repository: https://github.com/bag-man/giraffe-browseDemo versionAn example installation of the application is available at http://giraffe.owen.cymru, using a GFF and FASTA file of Escherichia coli from the European Nucleotide [email protected]

scholarly journals Web-based design and analysis tools for CRISPR base editing

2018 ◽  
Author(s):  
Gue-Ho Hwang ◽  
Jeongbin Park ◽  
Kayeong Lim ◽  
Sunghyun Kim ◽  
Jihyeon Yu ◽  
...  
Keyword(s):  
High Efficiency ◽  
Target Sequence ◽  
Sequencing Data ◽  
Gene Correction ◽  
Web Based ◽  
Base Editing ◽  
Link Type ◽  
Web Tools ◽  
A Genome ◽  
Ngs Data

AbstractBackgroundAs a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool. Recently, CRISPR base editors, which consist of deactivated Cas9 (dCas9) or Cas9 nickase (nCas9) linked with a cytidine or a guanine deaminase, have been developed. Base editing tools will be very useful for gene correction because they can produce highly specific DNA substitutions without the introduction of any donor DNA, but dedicated web-based tools to facilitate the use of such tools have not yet been developed.ResultsWe present two web tools for base editors, named BE-Designer and BE-Analyzer. BE-Designer provides all possible base editor target sequences in a given input DNA sequence with useful information including potential off-target sites. BE-Analyzer, a tool for assessing base editing outcomes from next generation sequencing (NGS) data, provides information about mutations in a table and interactive graphs. Furthermore, because the tool runs client-side, large amounts of targeted deep sequencing data (>100MB) do not need to be uploaded to a server, substantially reducing running time and increasing data security. BE-Designer and BE-Analyzer can be freely accessed at http://www.rgenome.net/bedesigner/ and http://www.rgenome.net/be-analyzer/respectivelyConclusionWe develop two useful web tools to design target sequence (BE-Designer) and to analyze NGS data from experimental results (BE-Analyzer) for CRISPR base editors.

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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