BackgroundAs large genomics and phenotypic datasets are becoming more common, it is increasingly difficult for most researchers to access, manage, and analyze them. One possible approach is to provide the research community with several petabyte-scale cloud-based computing platforms containing these data, along with tools and resources to analyze it.MethodsBionimbus is an open source cloud-computing platform that is based primarily upon OpenStack, which manages on-demand virtual machines that provide the required computational resources, and GlusterFS, which is a high-performance clustered file system. Bionimbus also includes Tukey, which is a portal, and associated middleware that provides a single entry point and a single sign on for the various Bionimbus resources; and Yates, which automates the installation, configuration, and maintenance of the software infrastructure required.ResultsBionimbus is used by a variety of projects to process genomics and phenotypic data. For example, it is used by an acute myeloid leukemia resequencing project at the University of Chicago. The project requires several computational pipelines, including pipelines for quality control, alignment, variant calling, and annotation. For each sample, the alignment step requires eight CPUs for about 12 h. BAM file sizes ranged from 5 GB to 10 GB for each sample.ConclusionsMost members of the research community have difficulty downloading large genomics datasets and obtaining sufficient storage and computer resources to manage and analyze the data. Cloud computing platforms, such as Bionimbus, with data commons that contain large genomics datasets, are one choice for broadening access to research data in genomics.

In this paper we describe the design, and implementation of the Open Science Data Cloud, or OSDC. The goal of the OSDC is to provide petabyte-scale data cloud infrastructure and related services for scientists working with large quantities of data. Currently, the OSDC consists of more than 2000 cores and 2 PB of storage distributed across four data centers connected by 10G networks. We discuss some of the lessons learned during the past three years of operation and describe the software stacks used in the OSDC. We also describe some of the research * Robert L. Grossman is the corresponding author.projects in biology, the earth sciences, and social sciences enabled by the OSDC.

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