Open and Free: Software and Scientific Reproducibility

Abstract

Recent scandals, retractions and proliferation of scientific research has reached a stage where scrutiny of scientific debate is now routinely reported in the public press as evidence of bungling, or, worse, dishonesty, in our profession (see Zimmer, 2012; Reay, 2010). High profile cases, like the discredited cancer research at Duke University or the notorious “Climate‐gate”, can be traced back to poor implementation of checks and balances on standard scientific practice. One remedy is to require researchers to use open methods of analysis, to share software, and to submit only reproducible analysis where it is feasible. Barriers to reproducibility are propriety (closed) software and computer platforms that encourage, rather than prevent, sloppy documentation. It is time to remind ourselves of efforts, perhaps started in the 1980’s, to reestablish standards of reproducibility (see Schwab et al. , 1996). It has been a couple years now that I have acted as editor‐in‐chief of SRL, Seismological Research Letters . In the capacity of editor I handle papers submitted by authors all over the world. Some time ago a paper came across my desk formatted with an older version of a very popular word processor. I will not mention any names, but this software is used, nearly universally, by scientists and professionals around the world. The paper included equations formatted with an outdated system, a set of routines supplied by the corporate software publisher of the word processor that have since been superseded by newer, costly upgrades. Since the submission was formatted in this manner, I could not …