Software paper

Promoting the tool you developed to access your data

November 2025

Nicolas Casajus

Senior data scientist
@FRB-CESAB    

Data lifecycle

Data lifecycle

Acknowledgments

This presentation is strongly inspired by the chapter Software papers of the online book The Turing Way.



The Turing Way Community (2021) The Turing Way: A handbook for reproducible, ethical and collaborative research. Zenodo. https://doi.org/10.5281/zenodo.3233853.

What is a software paper?

  • Share a new piece of software with the research community
  • Close to traditional method papers
  • Shorter than traditional articles (between 2 and 10 pages)
  • Focus on describing the software and its use

What is a software paper?

  • Share a new piece of software with the research community
  • Close to traditional method papers
  • Shorter than traditional articles (between 2 and 10 pages)
  • Focus on describing the software and its use


 Software paper about your pipeline

What is a software paper?

  • Share a new piece of software with the research community
  • Close to traditional method papers
  • Shorter than traditional articles (between 2 and 10 pages)
  • Focus on describing the software and its use


 Software paper about a tool to access data

What is a software paper?

  • Share a new piece of software with the research community
  • Close to traditional method papers
  • Shorter than traditional articles (between 2 and 10 pages)
  • Focus on describing the software and its use


 Software paper about a tool to add new data

Software papers - Examples

Software paper - Why?

  • Advertise your code to an interested audience
  • Increase the visibility of your code and community
  • Improve your software through peer-review

In which journals?

  • Methods in Ecology and Evolution   
  • Journal of Open Source Software (JOSS)   
  • Journal of Open Research Software (JORS)   
  • BMC Bioinformatics   
  • PeerJ   
  • PLOS Computational Biology: Software   
  • PLOS ONE   
  • …

Zoom on JOSS

Feedback on publishing in Journal of Open Source Software (JOSS)

https://github.com/frbcesab/chessboard/

https://joss.theoj.org/papers/10.21105/joss.05753

Thanks!