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Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

Konstantinos Krampis1*, Tim Booth2, Brad Chapman3, Bela Tiwari4, Mesude Bicak2, Dawn Field2 and Karen E Nelson1

Author affiliations

1 J.Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA

2 CEH Wallingford, Benson Lane, Wallingford, UK

3 Bioinformatics Core, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA

4 CLC Bio, Finlandsgade 10, 8200 Århus N, Denmark

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Citation and License

BMC Bioinformatics 2012, 13:42  doi:10.1186/1471-2105-13-42

Published: 19 March 2012

Abstract

Background

A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure.

Results

Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds.

Conclusions

Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them.