This article is part of the supplement: Proceedings of the 11th Annual Bioinformatics Open Source Conference (BOSC) 2010

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Galaxy CloudMan: delivering cloud compute clusters

Enis Afgan1, Dannon Baker1, Nate Coraor2, Brad Chapman3, Anton Nekrutenko2 and James Taylor1*

Author affiliations

1 Department of Biology and Department of Mathematics & Computer Science, Emory University, Atlanta, GA 30322, USA

2 Huck Institute for the Life Sciences, Penn State University, University Park, PA 16802, USA

3 Department of Molecular Biology, Simches Research Center, Massachusetts General Hospital, Boston, MA 02114, USA

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Citation and License

BMC Bioinformatics 2010, 11(Suppl 12):S4  doi:10.1186/1471-2105-11-S12-S4

Published: 21 December 2010



Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research. An alternative to building and maintaining local infrastructure is “cloud computing”, which, in principle, offers on demand access to flexible computational infrastructure. However, cloud computing resources are not yet suitable for immediate “as is” use by experimental biologists.


We present a cloud resource management system that makes it possible for individual researchers to compose and control an arbitrarily sized compute cluster on Amazon’s EC2 cloud infrastructure without any informatics requirements. Within this system, an entire suite of biological tools packaged by the NERC Bio-Linux team ( webcite) is available for immediate consumption. The provided solution makes it possible, using only a web browser, to create a completely configured compute cluster ready to perform analysis in less than five minutes. Moreover, we provide an automated method for building custom deployments of cloud resources. This approach promotes reproducibility of results and, if desired, allows individuals and labs to add or customize an otherwise available cloud system to better meet their needs.


The expected knowledge and associated effort with deploying a compute cluster in the Amazon EC2 cloud is not trivial. The solution presented in this paper eliminates these barriers, making it possible for researchers to deploy exactly the amount of computing power they need, combined with a wealth of existing analysis software, to handle the ongoing data deluge.