We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development.

SummaryA tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. These quadruplexes are able to form because guanine can Hoogsteen hydrogen bond to other guanines, and a tetrad of guanines can form a stable arrangement. Recently we have discovered that probes on Affymetrix GeneChips that contain runs of guanine do not measure gene expression reliably. We associate this finding with the likelihood that quadruplexes are forming on the surface of GeneChips.In order to cope with the rapidly expanding size of GeneChip array datasets in the public domain, we are exploring the use of cloud computing to replicate our experiments on 3 ′ arrays to look at the effect of the location of G-spots (runs of guanines). Cloud computing is a recently introduced high-performance solution that takes advantage of the computational infrastructure of large organisations such as Amazon and Google.We expect that cloud computing will become widely adopted because it enables bioinformaticians to avoid capital expenditure on expensive computing resources and to only pay a cloud computing provider for what is used. Moreover, as well as financial efficiency, cloud computing is an ecologically-friendly technology, it enables efficient data-sharing and we expect it to be faster for development purposes. Here we propose the advantageous use of cloud computing to perform a large data-mining analysis of public domain 3 ′ arrays.

Cloud based scientific data management -storage, transfer, analysis, and inference extraction -is attracting interest. In this paper, we propose a next generation cloud deployment model suitable for data intensive applications. Our model is a flexible and self-service container-based infrastructure that delivers -network, computing, and storage resources together with the logic to dynamically manage the components in a holistic manner. We demonstrate the strength of our model with a bioinformatics application. Dynamic algorithms for resource provisioning and job allocation suitable for the chosen dataset are packaged and delivered in a privileged virtual machine as part of the container. We tested the model on our private internal experimental cloud that is built on low-cost commodity hardware. We demonstrate the capability of our model to create the required network and computing resources and allocate submitted jobs. The results obtained shows the benefits of increased automation in terms of both a significant improvement in the time to complete a data analysis and a reduction in the cost of analysis. The algorithms proposed reduced the cost of performing analysis by 50% at 15 GB of data analysis. The total time between submitting a job and writing the results after analysis also reduced by more than 1 hr at 15 GB of data analysis.

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