Progressive development environments: Scaffolding computational competency in research teams

Computational Immunology increasingly requires computational skills embedded in Immunological research teams. However, team members at varying stages of their careers present with vastly different programming competencies. Siloed tools risk stagnating beginners with overly simple tools or overwhelm them with stack knowledge dependencies. This talk presents our systematic approach to a progressive development environment that scaffolds researchers from initial computational literacy through to robust, collaborative coding practices.Our framework begins with simple notebooks with preconfigured environments, where researchers can focus on domain problems rather than tooling complexity. We then guide users through structured transitions: converting exploratory cells into reusable functions, extracting functions into importable modules, and ultimately migrating to integrated development environments like VSCode or Cursor with full version control workflows using Git.Operating as a small support team, this approach enables researchers to self-serve their day-to-day computational needs while gradually adopting industry-standard development practices. We complement the technical progression with open forums and peer learning sessions that build both technical skills and collaborative research culture. The advent of LLM’s has assisted greatly in permitting novice programmers to generate functional scripts and we strike a balance between this short-term catalyst and the need for robust and understood code.This talk will demonstrate key features of each environment stage, discuss workflow transition strategies, and share lessons learned from supporting diverse research teams in developing sustainable computational practices.ABOUT THE AUTHORDr. Joshua Duley works as the Senior Data Scientist working in the Hugh Green Technology Center within the Malaghan Institute of Medical Research. His work assists the analytical goals of researchers and support teams across the institute. His background in applied mathematics and industrial consulting have built a flexible and outcome oriented style of work seeking to get collaborators converting on projects as efficiently as possible. -----For more information about the eResearch NZ / eRangahau Aotearoa conference, visit: https://eresearchnz.co.nz/