Reproducing Bioinformatics Experiments: A Case Study Using the Environment Code-First Framework

Verifying published findings in bioinformatics through independent validation is challenging, mainly when accounting for differences in software and hardware to recreate computational environments. Reproducing a computational environment that closely mimics the original proves intricate and demands a significant investment of time. In this paper, we present a case study on how a recently proposed reproducibility framework named Environment Code-First (ECF) based on the Infrastructure-as-Code approach can improve the implementation and reproduction of computing environments by reducing complexity and manual intervention. We detail the steps needed to implement the computational environment of a bioinformatics pipeline named MetaWorks from the perspective of the scientist who owns the research work. Also, we present the steps taken to recreate the environment from the point of view of one who wants to reproduce the published results of a research work. This exercise compares the manual way of implementing the pipeline and the automated method proposed by the ECF framework, showing real metrics regarding time consumption, efforts, manual intervention, and platform agnosticism.