Forking software used in eLife papers to GitHub

As part of our mission to support reproducibility, eLife is now using GitHub to ensure the version of cited code within an article persists.
Inside eLife

By Maria Guerreiro, Senior Editorial Assistant, eLife

Since it was launched in 2008, the version-control repository and hosting service GitHub has not only been a vital tool in the daily life of programmers and developers, but it has also become increasingly important for researchers in the biomedical and life sciences. The influence of GitHub has grown significantly, with more than 56 million projects hosted (as of April 2017), and increasingly published papers include citations to GitHub (Jeffrey Perkel, "Democratic databases: science on GitHub", Nature, 2016).

GitHub and other hosting services for git repositories, such as SourceForge or GitLab, facilitate collaboration, while ensuring at the same time that any changes made in the code are recorded and documented properly.

In line with eLife's aims to encourage more open and reproducible science, we have created a GitHub account to track new software or a new algorithm when they are central to the submission and to make sure that the right version of the code that was used within an article persists. When a paper is accepted in eLife, if the authors have included a link to code within GitHub, a copy of the authors' repository is "forked" (cloned) to the eLife GitHub account, with a clear link to the authors' original repository. This means that we can keep an archive of the version of the code that was issued at the point of publication and that the authors, as well as the community, can continue to build upon the work in their own repositories. If authors have used another version control system, a copy of the code will also be added into the eLife GitHub account.

Jan Willem de Gee (University Medical Center Hamburg-Eppendorf), one of the first eLife authors to have code included within eLife’s GitHub account, said: "I think it's really great the way eLife promotes accessibility, transparency and reproducibility; it was our pleasure to contribute."

In addition to eLife forking the code at acceptance, authors are also asked to include their GitHub repositories in the references list and cite the last commit tracking number. Software should comply with the Open Source Definition and should use an open-source license, such as MIT, GNU/GPL, BSD, and so on, so that others can easily access and reuse the software, and authors get the credit they deserve for this part of their work.

Well documented and open software help to support reproducible science and we encourage researchers to prepare their software for a seamless and straightforward application by others.

Richard Neher from the University of Basel and an Associate Editor at eLife, who suggested that eLife should maintain a copy of the code that accompanies publications, said: “Scripts and software have become an integral part of many papers. I hope that the new eLife policy to fork code will promote reproducibility, facilitate reuse, and encourage authors to document their code.”

We welcome comments/questions from researchers as well as other journals. Get in touch with staff [at] elifesciences [dot] org. To keep up-to-date with all technology related efforts at eLife, sign up for our bimonthly technology and innovation newsletter.