Dataset Information

MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data.

ABSTRACT:

Background

The rapid identification of pathogen clones is pivotal for effective epidemiological control strategies in hospital settings. High Resolution Melting (HRM) is a molecular biology technique suitable for fast and inexpensive pathogen typing protocols. Unfortunately, the mathematical/informatics skills required to analyse HRM data for pathogen typing likely limit the application of this promising technique in hospital settings.

Results

MeltingPlot is the first tool specifically designed for epidemiological investigations using HRM data, easing the application of HRM typing to large real-time surveillance and rapid outbreak reconstructions. MeltingPlot implements a graph-based algorithm designed to discriminate pathogen clones on the basis of HRM data, producing portable typing results. The tool also merges typing information with isolates and patients metadata to create graphical and tabular outputs useful in epidemiological investigations and it runs in a few seconds even with hundreds of isolates.

Availability

https://skynet.unimi.it/index.php/tools/meltingplot/ .

Conclusions

The analysis and result interpretation of HRM typing protocols can be not trivial and this likely limited its application in hospital settings. MeltingPlot is a web tool designed to help the user to reconstruct epidemiological events by combining HRM-based clustering methods and the isolate/patient metadata. The tool can be used for the implementation of HRM based real time large scale surveillance programs in hospital settings.

SUBMITTER: Perini M

PROVIDER: S-EPMC7891011 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Publications

MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data.

Perini Matteo M Batisti Biffignandi Gherard G Di Carlo Domenico D Pasala Ajay Ratan AR Piazza Aurora A Panelli Simona S Zuccotti Gian Vincenzo GV Comandatore Francesco F

BMC bioinformatics 20210218 1

<h4>Background</h4>The rapid identification of pathogen clones is pivotal for effective epidemiological control strategies in hospital settings. High Resolution Melting (HRM) is a molecular biology technique suitable for fast and inexpensive pathogen typing protocols. Unfortunately, the mathematical/informatics skills required to analyse HRM data for pathogen typing likely limit the application of this promising technique in hospital settings.<h4>Results</h4>MeltingPlot is the first tool specifi ...[more]

PMID: 33602119

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Project description:BackgroundExplosive growth of next-generation sequencing data has resulted in ultra-large-scale data sets and ensuing computational problems. Cloud computing provides an on-demand and scalable environment for large-scale data analysis. Using a MapReduce framework, data and workload can be distributed via a network to computers in the cloud to substantially reduce computational latency. Hadoop/MapReduce has been successfully adopted in bioinformatics for genome assembly, mapping reads to genomes, and finding single nucleotide polymorphisms. Major cloud providers offer Hadoop cloud services to their users. However, it remains technically challenging to deploy a Hadoop cloud for those who prefer to run MapReduce programs in a cluster without built-in Hadoop/MapReduce.ResultsWe present CloudDOE, a platform-independent software package implemented in Java. CloudDOE encapsulates technical details behind a user-friendly graphical interface, thus liberating scientists from having to perform complicated operational procedures. Users are guided through the user interface to deploy a Hadoop cloud within in-house computing environments and to run applications specifically targeted for bioinformatics, including CloudBurst, CloudBrush, and CloudRS. One may also use CloudDOE on top of a public cloud. CloudDOE consists of three wizards, i.e., Deploy, Operate, and Extend wizards. Deploy wizard is designed to aid the system administrator to deploy a Hadoop cloud. It installs Java runtime environment version 1.6 and Hadoop version 0.20.203, and initiates the service automatically. Operate wizard allows the user to run a MapReduce application on the dashboard list. To extend the dashboard list, the administrator may install a new MapReduce application using Extend wizard.ConclusionsCloudDOE is a user-friendly tool for deploying a Hadoop cloud. Its smart wizards substantially reduce the complexity and costs of deployment, execution, enhancement, and management. Interested users may collaborate to improve the source code of CloudDOE to further incorporate more MapReduce bioinformatics tools into CloudDOE and support next-generation big data open source tools, e.g., Hadoop BigTop and Spark.AvailabilityCloudDOE is distributed under Apache License 2.0 and is freely available at http://clouddoe.iis.sinica.edu.tw/.

Dataset Information

MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data.

Background

Results

Availability

Conclusions

Publications

MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data.

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