Building an Interactive Workbench Environment for Single Cell Genomics Applications

We discuss the procedure to build an interactive workbench environment for single cell genomics applications with the Open OnDemand (OOD) science gateway. In our approach, an end-user submits a complex single cell RNA sequencing (scRNA) pipeline, checks the status of the job, and visualizes the output results. All of these tasks are accomplished through a web browser, relieving the users from the complexities involved in developing and handling a large-scale workflow. Our approach helped researchers in processing several input data sets of scRNA in the campus HPC cluster. Although the current work is focused on scRNA analysis, the same approach can be extended for any workflow.