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RBioCloud: A Light-Weight Framework for Bioconductor and R-based Jobs on the Cloud | JoVE Visualize

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RBioCloud: A Light-Weight Framework for Bioconductor and R-based Jobs on the Cloud

Blesson Varghese, Ishan Patel, Adam Barker

IEEE/ACM Transactions on Computational Biology and Bioinformatics|September 11, 2015

View abstract on PubMed

Summary

This study introduces RBioCloud, a framework simplifying cloud execution for R-programming language and Bioconductor packages in genomic data analysis. It enables easy management of cloud resources and data for biologists and bioinformaticists.

Area of Science:

Bioinformatics
Computational Biology
Genomic Data Analysis

Background:

Genomic data analysis commonly utilizes the R-programming language with Bioconductor packages.
Cloud computing offers scalable, cost-effective solutions for analytical jobs.
Executing R/Bioconductor jobs on cloud infrastructure is challenging without specialized knowledge.

Purpose of the Study:

To explore seamless execution of analytical jobs on cloud infrastructure with minimal user effort.
To provide methods for managing cloud resources and data required for analytical jobs.
To introduce a framework for simplifying cloud-based R and Bioconductor package execution.

Main Methods:

Development of an open-source, lightweight framework named RBioCloud.
RBioCloud provides command-line tools for managing cloud resources, data, and job execution.
Validation of the framework's feasibility through three biological test cases.

Main Results:

Successful development and validation of the RBioCloud framework.
Demonstrated ability of RBioCloud to simplify cloud execution of R/Bioconductor jobs.
Effective management of cloud resources and data for genomic analyses.

Conclusions:

RBioCloud facilitates the execution of R-scripts and Bioconductor packages on cloud platforms.
The framework lowers the barrier for biologists and bioinformaticists to leverage cloud computing.
RBioCloud offers a practical solution for scalable and manageable genomic data analysis in the cloud.

Distributed Computing And Systems Software

Energy-efficient Computing

Rbiocloud: A Light-weight Framework For Bioconductor And R-based Jobs On The Cloud