PyRDM: A Python-based library for automating the management and online publication of scientific software and data
PyRDM: A Python-based library for automating the management and online publication of scientific software and data
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.
scientific software, data, automated publication, reproducibility, recomputability, python, figshare, GitHub
1-6
Jacobs, Christian T.
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Avdis, Alexandros
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Gorman, Gerard J.
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Piggott, Matthew D.
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3 October 2014
Jacobs, Christian T.
7c66a8a5-7b13-4511-8946-20149fe188d9
Avdis, Alexandros
b88cf33e-e109-4ea2-bd4f-1aaf42e24e59
Gorman, Gerard J.
12156f2f-fa24-4704-907d-3307917d528e
Piggott, Matthew D.
ecfbaf4c-61ab-4a5e-82af-fdd9e34f36c8
Jacobs, Christian T., Avdis, Alexandros, Gorman, Gerard J. and Piggott, Matthew D.
(2014)
PyRDM: A Python-based library for automating the management and online publication of scientific software and data.
Journal of Open Research Software, 2 (1), .
(doi:10.5334/jors.bj).
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.
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Published date: 3 October 2014
Keywords:
scientific software, data, automated publication, reproducibility, recomputability, python, figshare, GitHub
Organisations:
Physics & Astronomy
Identifiers
Local EPrints ID: 394553
URI: http://eprints.soton.ac.uk/id/eprint/394553
PURE UUID: e5c57003-75ea-4155-9b5a-707f0030f90a
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Date deposited: 17 May 2016 09:31
Last modified: 15 Mar 2024 00:26
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Contributors
Author:
Christian T. Jacobs
Author:
Alexandros Avdis
Author:
Gerard J. Gorman
Author:
Matthew D. Piggott
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