Leveraging iPlant Cyberinfrastructure for a New Data-Driven Research Community

Data storage, high-performance computing, and analysis pipelines represent the major computational resources that are required in many areas of data-driven research. Yet these resources are limited in availability, and therefore, many investigations are restricted to the commercial sector or well-funded academic programs. To address this challenge, the cyberinfrastructure developed by the iPlant Collaborative (NSF-#DBI0735191) and its extension iAnimal (USDA-#2013-67015-21231) provides a straightforward approach for the storage, sharing, and analyses of large datasets – from genomes to phenotype data and beyond – all accessible via a comprehensive and freely available platform. Significantly, this platform is designed from the ground up to support a variety of research communities, each with their particular focus and customized needs for software tools and data sharing.  Here we demonstrate how this community-based approach was applied to quickly develop scalable, accessible versions of common workflows required for applying genome re-sequencing to livestock genomics (variant calling). This has important consequences as whole genome sequences, SNPs, copy number variation, phenotypes and other “-omics” data underlie evidence-based estimations of breeding value. The iPlant/iAnimal tools developed here support a variety of genotype-phenotype related analyses in a platform that accommodates every level of user – from breeder to bioinformatician – thus providing the animal breeding community with a comprehensive and freely available resource for their data-driven research.