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

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 substant...

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Vydané v:BMC bioinformatics Ročník 13; číslo 1; s. 42
Hlavní autori: Krampis, Konstantinos, Booth, Tim, Chapman, Brad, Tiwari, Bela, Bicak, Mesude, Field, Dawn, Nelson, Karen E
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 19.03.2012
BioMed Central Ltd
Springer Nature B.V
BMC
Predmet:
Algorithms
Animals
Bioinformatics
Biomedical and Life Sciences
Cloud computing
Clouds
Computational biology
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer applications
Computer graphics
Computer programs
Computers
Computing Methodologies
Data processing
Documentation
Eucalyptus
Forecasts and trends
Genomics
Genomics - methods
Humans
Informatics
Life Sciences
Microarrays
Nucleotide sequence
Phylogeny
Sequence Alignment
Sequence analysis (methods)
Software
Storage capacity
Technology application
United States
Cloud Platform
Cloud Computing
Configuration File
Private Cloud
Virtual Machine
ISSN:1471-2105, 1471-2105
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Shrnutí: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.
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ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-13-42