Leverage iPlant Computing Resources for Collaborative Genomic Research

The ability to sequence novel genomes using high-throughput methods has tremendously enabled the decoding of biological information to many research labs and investigators. The “democratization” of sequencing notwithstanding, the processing and data mining of the large amounts of sequences require massive computing and storage resources and technical know-hows. The iPlant collaborative has built a dedicated platform to distribute these resources to a wide range of researchers, small labs and large genome centers alike. With the help of iPlant and Texas Advanced Computing Center (TACC) staffs, we now have access to many more high-RAM servers and computing farms for the rapid production of large genome assemblies and annotations. We have compiled the Celera Assembler (CA) and MAKER pipelines as VMs that can be run on Atmosphere – the iPlant’s cloud computing solution. The Atmosphere images provide unique mechanism to quickly distribute working pipelines for common analyses tasks, such as genome assembly and annotation, which are relatively difficult for small labs to install and configure. Through connections to other researchers facing similar problems, iPlant connects researchers on the “social” level and greatly enhances the experience of sharing of methodology and data. Additionally, we believe that genome centers, such as JCVI, need to take more active role in working with iPlant to transfer the technical know-hows into an open cloud-based domain and gradually move away from the institutional legacy systems which are less transparent and un-sustainable in the long run.