Software paper

Making research software visible, citable and reusable

November 2026

Nicolas Casajus

Senior data scientist
@FRB-CESAB    

Data lifecycle

Data lifecycle

Software as a research output

• Research projects produce more than scientific publications and datasets

• Software plays a central role in:

  • Data collection and acquisition
  • Data cleaning and transformation
  • Data analysis and visualisation
  • Modelling and simulation

  However, software is often less documented, shared and recognised than data or publications

Software is a valuable research output
in its own right

Software and the FAIR-CARE Principles

Source: https://fair-software.nl/

Source: https://doi.org/10.1038/s41597-022-01710-x

Before publishing a Software paper

	Dimension	What should be in place?	Examples / Tools
	Version control	Commit history, releases	Git
	Code source	Public repository	GitHub, GitLab, Codeberg
	Archiving	Long-term preservation	Zenodo, Software Heritage
	Identification	Persistent & unique identifier	DOI, SWHID
	Documentation	Installation, documentation, usage	README, Website, Vignettes
	License	Explicit open-source licence	GPL, MIT, Apache 2.0
	Authorship	Maintainer, contributors & authors	ORCID, ROR, roles
	Citation metadata	Structured citation information	CITATION.cff, Codemeta
	Quality	Unit tests, CI/CD	testthat, GitHub Actions
	Community	Contribution guidelines, code of conduct	CONTRIBUTING.md, CODE_OF_CONDUCT.md

What is a Software Paper?

• A scientific peer-reviewed publication whose primary focus is a software application or tool

• It describes:

  • the scientific context and the problem addressed
  • the purpose and main functionalities of the software
  • its architecture and technical design
  • the methods and algorithms implemented
  • installation requirements and dependencies

Why publish a Software paper?

Visibility

Make research software discoverable
by the scientific community

Recognition

Give credit to software developers
and contributors

Traceability

Establish a link between software
and scientific publications

Reproducibility

Document methods, workflows and
execution conditions

Reusability

Enable other teams to understand,
test and adapt the software

Software paper, Data paper and co

Research article

Why was the research conducted,
and what were the findings?

Data paper

What data were produced, and how
are they structured and documented?

Methods paper

What method was developed, why was it designed, and how can it be applied?

Software paper

What software was developed, how
does it work, and how can it be reused?

Same research ecosystem
Complementary outputs

Example w/ the FORCIS project

  A FRB-CESAB research project on Foraminifera response to climatic stress   

7 x Research articles

Published in various journals
(Science, Nature, J. of Biogeography, etc.)

1 x Database

Released as a collection of CSV files
and archived on Zenodo  

1 x Data paper

Peer-reviewed and published in
Scientific Data  

1 x R Package

Peer-reviewed by rOpenSci  
and archived on CRAN  

1 x Software paper

Peer-reviewed and published in
Journal of Open Source Software  

Where can you publish a Software paper?

• Journals dedicated to research software

  • Journal of Open Source Software   
  • Journal of Open Research Software   
  • SoftwareX   

• Ecology-focused journals

  • Methods in Ecology and Evolution   
  • Ecology and Evolution   
  • Ecography   
  • PLOS Ecosystems   

• Broader journals accepting software papers

  • BMC Bioinformatics   
  • PLOS Computational Biology   
  • PLOS ONE   
  • PeerJ   

Take home message

Publishing research software helps preserving an essential part of the scientific process

Resources

• Tools & resources

  • Choose a license  
  • Zenodo  
  • Software Heritage  
  • Citation File Format (CFF)  
  • The CodeMeta Project  
  • Five recommendations for FAIR software  

• Writing Software papers

  • JOSS guidelines  
  • MEE guidelines  
  • Software papers in The Turing Way  

• Selected papers

  • Introducing the FAIR Principles for research software  
  • CODE beyond FAIR: A roadmap for reusable research software