Software paper

Promoting the tool you developed to access your data

October 2024

Nicolas Casajus

Senior data scientist
@FRB-CESAB    

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

But wait! What does this have to do with the 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

But wait! What does this have to do with the data?

 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

But wait! What does this have to do with the data?

 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

But wait! What does this have to do with the data?

 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!