Examples
Worked examples
- Is an instance
A study's analysis scripts published on GitHub and archived in Zenodo with DOI on paper acceptance.
- Is an instance
A bioinformatics pipeline released under MIT licence with a CITATION.cff file.
Counter-examples
Looks similar, but isn't
- Not an instance
Code 'available on reasonable request'.
- Not an instance
Pseudocode in a methods section.
Editorial commentary
Open code is the practice of releasing the source code used to process and analyse a study’s data — scripts, pipelines, notebooks — under an open-source licence alongside the publication, so that any reader can inspect exactly what was computed and re-execute the analysis rather than relying on a prose description of the method. It is a necessary condition for computational reproducibility: even a fully open dataset cannot be independently checked if the specific transformations, model specifications, and exclusion rules applied to it are not themselves available for inspection.
Established good practice combines several elements: a version-controlled repository (typically Git, hosted on GitHub or GitLab); a permanent archival snapshot taken at the time of publication (via Zenodo or Software Heritage, since a live repository can be edited, renamed, or deleted after the fact); an explicit open-source licence (MIT, BSD, GPL, and Apache-2.0 are the most common in research code); and a machine-readable citation file (CITATION.cff) so the software itself can be cited properly.
Why “available on request” does not count
Code described in a paper as “available from the authors on reasonable request,” or presented only as pseudocode in a methods section, does not meet the open-code standard: both leave a reader dependent on the original authors’ continued willingness and availability, rather than providing an independently accessible, citable artefact. A growing number of journals now decline this wording outright for both code and data availability statements. Journals implementing the TOP Guidelines' Analytic Methods (Code) Transparency standard grade exactly this: the higher levels require deposit in a trusted repository, not a promise of availability. Open code is a separate practice from open data (the inputs) and open materials (the instruments used to generate those inputs) — a study can release any one of the three without the others, though reproducibility is strongest when all three are present together.
References
- Barba, 'Terminologies for Reproducible Research' (arXiv, 2018).
- FORCE11 Software Citation Principles.
Also known as
open-source research code · shared analysis code
Machine-readable encodings
Use in your systems
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