A New Way to Produce Research Papers


David Mawdsley, a Research software engineer (RSE) in Research IT, presented at the recent Docker Containers for Reproducible Research Workshop (C4RR) organised by the Software Sustainability Institute.

His presentation described a new method of producing research papers using containerisation, which makes both the analysis and manuscript easy to produce and extend.  This can be used as a starting point for a new, versioned publication model, which will allow early publication of results and their incremental extension.

The team used Docker images to provide a reproducible analysis pipeline, together with Knitr, an R package that allowed the combining of R and other code with LaTeX in an extensible and transparent way. The advantage of this system is that it integrates the manuscript production into the analysis pipeline, while allowing others to verify the results of a paper, and potentially modify or extend the analysis. By doing this a reproducible paper is generated where calculations in the analysis code are automatically reflected in the manuscript text.

The work was done in conjunction with the Idinteraction team in Computer Science where David has been hired to provide data analysis expertise to the group.  If you would like to know more about this work or hiring an RSE to contribute to your research project, please contact Robert Haines, Head of Research Software Engineering, Research IT.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s