N3phele: Open Science-as-a-Service Workbench for Cloud-based Scientific Computing

Because of inexpensive, on-demand resources, Cloud computing is a promising platform for scientific HPC applications, such as gene sequencing. However, it also poses challenges to users and developers in terms of running and maintaining HPC applications which is low-level and complex for scientists. This impacts reusability and reproducibility of the work and increases the cost of development and maintenance. N3phele is a cloud-based workbench that allows researchers to perform complex analysis using only browser and resources in infrastructure clouds, which are orchestrated by n3phele. Individual scientists may publish tools and workflow pipelines, registering them in n3phele for their own private or public collaborator use. To illustrate, the QIIME microbial community analysis toolkit has been registered into n3phele, and n3phele used to perform microbial analysis, including computationally intensive Roche 454 denoising, using Amazon EC2 and n3phele's point and click interface. N3phele substantially improves usability and manageability of complex scientific analysis pipelines in the cloud.