Biblio

Science gateways bring out the possibility of reproducible science as they are integrated into reusable techniques, data and workflow management systems, security mechanisms, and high performance computing (HPC). We introduce BioinfoPortal, a science gateway that integrates a suite of different bioinformatics applications using HPC and data management resources provided by the Brazilian National HPC System (SINAPAD). BioinfoPortal follows the Software as a Service (SaaS) model and the web server is freely available for academic use. The goal of this paper is to describe the science gateway and its usage, addressing challenges of designing a multiuser computational platform for parallel/distributed executions of large-scale bioinformatics applications using the Brazilian HPC resources. We also present a study of performance and scalability of some bioinformatics applications executed in the HPC environments and perform machine learning analyses for predicting features for the HPC allocation/usage that could better perform the bioinformatics applications via BioinfoPortal.

The Agave Platform first appeared in 2011 as a pilot project for the iPlant Collaborative [11]. In its first two years, Foundation saw over 40% growth per month, supporting 1000+ clients, 600+ applications, 4 HPC systems at 3 centers across the US. It also gained users outside of plant biology. To better serve the needs of the general open science community, we rewrote Foundation as a scalable, cloud native application and named it the Agave Platform. In this paper we present the Agave Platform, a Science-as-a-Service (ScaaS) platform for reproducible science. We provide a brief history and technical overview of the project, and highlight three case studies leveraging the platform to create synergistic value for their users.