Recommendations to enhance rigor and reproducibility in biomedical research

Abstract: Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably enforced by academic institutions, funders, and publishers. Publications may present academic software for which essential materials are or become unavailable, such as source code and documentation. Publications that lack such information compromise the role of peer review in evaluating technical strength and scientific contribution. Incomplete ancillary information for an academic software package may bias or limit any subsequent work produced with the tool. We provide eight recommendations across four different domains to improve reproducibility, transparency, and rigor in computational biology - precisely on the main values which should be emphasized in life science curricula. Our recommendations for improving software availability, usability, and archival stability aim to foster a sustainable data science ecosystem in biomedicine and life science research.