PyRDM: A Python-based library for automating the management and online publication of scientific software and data
Abstract
The recomputability and reproducibility of results from scientific software requires access to both the source code and all associated input and output data. However, the full collection of these resources often does not accompany the key findings published in journal articles, thereby making it difficult or impossible for the wider scientific community to verify the correctness of a result or to build further research on it. This paper presents a new Python-based library, PyRDM, whose functionality aims to automate the process of sharing the software and data via online, citable repositories such as Figshare. The library is integrated into the workflow of an open-source computational fluid dynamics package, Fluidity, to demonstrate an example of its usage.
Keywords
Cite
@article{arxiv.1405.7290,
title = {PyRDM: A Python-based library for automating the management and online publication of scientific software and data},
author = {Christian T. Jacobs and Alexandros Avdis and Gerard J. Gorman and Matthew D. Piggott},
journal= {arXiv preprint arXiv:1405.7290},
year = {2015}
}
Comments
Revised version. The main changes are: Added pdfLaTeX to the dependencies list; Improved Figure 1 to show the 'publish' option selected in Diamond; Added two paragraphs to explain why users would want to use PyRDM; Added some content on the PyRDM roadmap, and also some content regarding engagement with libraries and research software engineers