A survey of code sharing practice and policy in computational biology

Sharing of code supports reproducible research but fewer journals have policies on code sharing compared to data sharing, and there is little evidence on researchers’ attitudes and experiences with code sharing. Before introducing a stronger policy on sharing of code, the Editors and publisher of the journal PLOS Computational Biology wished to test, via an online survey, the suitability of a proposed mandatory code sharing policy with its community of authors. Previous research has established, in 2019, 41% of papers in the journal linked to shared code. We also wanted to understand the potential impact of the proposed policy on authors' submissions to the journal, and their concerns about code sharing.We received 214 completed survey responses, all of whom had generated code in their research previously. 80% had published in PLOS Computational Biology and 88% of whom were based in Europe or North America. Overall, respondents reported they were more likely to submit to the journal if it had a mandatory code sharing policy and US researchers were more positive than the average for all respondents. Researchers whose main discipline is Medicine and Health sciences viewed the proposed policy less favourably, as did the most senior researchers (those with more than 100 publications) compared to early and mid-career researchers.The authors surveyed report that, on average, 71% of their research articles have associated code, and that for the average author, code has not been shared for 32% of these papers. The most common reasons for not sharing code previously are practical issues, which are unlikely to prevent compliance with the policy. A lack of time to share code was the most common reason. 22% of respondents who had not shared their code in the past cited intellectual property (IP) concerns - a concern that might prevent public sharing of code under a mandatory code sharing policy. The results also imply that 18% of the respondents’ previous publications did not have the associated code shared and IP concerns were not cited, suggesting more papers in the journal could share code.To remain inclusive of all researchers in the community, the policy was designed to allow researchers who can demonstrate they are legally restricted from sharing their code to be granted an exemption to public sharing of code.As a secondary goal of the survey we wanted to determine if researchers have unmet needs in their ability to share their own code, and to access other researchers' code. Consistent with our previous research on data sharing, we found potential opportunities for new products or features that support code accessibility or reuse. We found researchers were on average satisfied with their ability to share their own code, suggesting that offering new products or features to support sharing in the absence of a stronger policy would not increase the availability of code with the journal's publications.