A path to next-generation reproducibility in cheminformatics

Abstract

Currently, the submission guidelines for the Journal of Cheminformatics say it will “only publish research or software that is entirely reproducible by third parties.” They go on to specify that being reproducible means that anything essential to the conclusion of the paper be freely accessible and states that source code must be provided. I submit that this definition of reproducibility is too narrow—that a cheminformatics method can only truly be replicated by reimplementing it from a detailed, step-by-step high-level description to determine how reliably the algorithm per se does what it is intended to do.