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Cloudgene: a graphical execution platform for MapReduce programs on private and public clouds.

Sebastian Schönherr1, Lukas Forer, Hansi Weißensteiner

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BMC Bioinformatics
|August 15, 2012
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Summary
This summary is machine-generated.

Cloudgene simplifies using MapReduce for bioinformatics by offering a graphical interface for data processing and workflow reproducibility. This platform makes complex MapReduce programs accessible to scientists, enhancing bioinformatics research.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Data Science

Background:

  • The MapReduce framework facilitates scalable processing of large datasets across computer clusters.
  • MapReduce applications in bioinformatics include genome mapping and SNP detection.
  • Complexities in MapReduce setup and usage hinder adoption by scientists.

Purpose of the Study:

  • To present Cloudgene, a platform enhancing MapReduce usability in bioinformatics.
  • To provide a graphical user interface for MapReduce program execution and data management.
  • To enable reproducible bioinformatics workflows on private and public clouds.

Main Methods:

  • Development of Cloudgene, a platform with a plug-in architecture for integrating MapReduce programs.
  • Implementation of a graphical user interface for data import/export and workflow execution.
  • Deployment on both in-house (private) and rented (public) cloud clusters.

Main Results:

  • MapReduce programs integrate into Cloudgene with minimal effort and no computational overhead.
  • Cloudgene offers a standardized graphical environment, abstracting MapReduce complexity for users.
  • Sensitive datasets can be processed on private clusters, minimizing data transfer times.

Conclusions:

  • Cloudgene successfully integrates MapReduce bioinformatics tools, improving accessibility for researchers.
  • The platform supports the execution of predefined systems like Cloud BioLinux and RStudio.
  • Cloudgene is freely available, fostering wider adoption of advanced computational methods in life sciences.