Streamlining Genomics Workflows Navigating Technology & Skill Limitations

As University of Melbourne students working on the Genomics Metadata Multiplexing (GMM) project at Walter and Eliza Hall Institute, we’d like to share our experience navigating the challenges of improving research software workflows while working within real-world constraints. We inherited a collection of scripts and prototypes from previous cohorts, each tackling different aspects of FACS file processing for genomics research. Our task was to consolidate these efforts into something more usable for researchers, but we quickly discovered the challenges of working with limited technical resources, varying skill levels across team members, and tight project timelines. This presentation will walk through our approach to consolidating Flask and R-based solutions into a single R Shiny application while managing these constraints. We’ll discuss how technology limitations shaped our decisions, how we adapted to different team members’ programming backgrounds, and the creative solutions we found when ideal approaches weren’t feasible. Key insights include: working within deployment constraints rather than fighting them, leveraging team members’ diverse strengths instead of expecting uniform expertise, and building incrementally when resources are limited. We’ll demonstrate our current workflow automation tool and share practical lessons about making progress despite imperfect conditions. This presentation is aimed at fellow students, early-career RSEs, and anyone working on research software projects with limited resources.