Examples
Worked examples
- Is an instance
A JOSS paper describing a Python package for single-cell sequencing analysis, reviewed openly on GitHub
Counter-examples
Looks similar, but isn't
- Not an instance
A research article that uses an existing software tool is not a software paper
Editorial commentary
A software paper is a peer-reviewed scholarly publication whose primary subject is a research software package itself — describing its functionality, architecture, dependencies, and testing, and its intended uses — rather than a scientific finding produced using that software. It is published in a venue that specifically issues this format, most notably the Journal of Open Source Software (JOSS) and SoftwareX, and accompanies the software’s own citable release in a code repository.
How this differs from an ordinary research article that uses software
A research article that applies an existing software tool to answer a scientific question is not a software paper — the software paper’s own subject is the software. JOSS’s review process is notably open (conducted on GitHub) and evaluates the software’s quality directly: whether it has adequate tests, documentation, and a clear open-source license, rather than assessing the novelty of any scientific results produced with it. JOSS explicitly accepts non-code contributions such as active project direction as a sufficient basis for authorship, reflecting how differently software-paper authorship criteria are drawn compared with a standard research-article byline.
Example
A JOSS paper describing a software package’s purpose, installation, and API, reviewed openly on GitHub against a checklist covering functionality, tests, and documentation, and published alongside a citable archived release of the code itself (commonly via Zenodo).
Also known as
Software descriptor · Research software paper
Machine-readable encodings
Use in your systems
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