AbSolution and ENCORE: a proof-of-concept for automating computational reproducibility in interactive applications

Reproducibility and transparency in computational analyses are essential in science, although achieving these goals often requires significant knowledge and systematic organization. Graphical interactive applications simplify the conduct of analyses and make them accessible to a broader audience. However, there is currently no consensus on how to and to which extent implement reproducibility in interactive applications. We recently developed AbSolution, a user-friendly and flexible interactive web-based R Shiny application for exploring immune repertoires and their sequence-based features, and we established the ENCORE framework to enhance transparency and reproducibility by guiding researchers in structuring and documenting computational projects. In this work, as a proof-of-concept we integrate AbSolution, ENCORE and specific R packages to address reproducibility challenges. This enables a single-step export of raw, processed, and meta-data, the software environment, the underlying generated code and a HTML report containing results and figures, operating system, hardware and R session details, and researcher notes. Its reproducibility has been independently validated by the CODECHECK initiative. This paper demonstrates how the combination of several approaches can improve and automate reproducibility of interactive applications.