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Storing Reproducible Results from Computational Experiments using Scientific Python Packages

Christian Schou Oxvig
Faculty of Engineering and Science, Department of Electronic Systems, Aalborg University, 9220 Aalborg, Denmark

Thomas Arildsen
Faculty of Engineering and Science, Department of Electronic Systems, Aalborg University, 9220 Aalborg, Denmark

Torben Larsen
Faculty of Engineering and Science, Department of Electronic Systems, Aalborg University, 9220 Aalborg, Denmark

Abstract

Computational methods have become a prime branch of modern science. Unfortunately, retractions of papers in high-ranked journals due to erroneous computations as well as a general lack of reproducibility of results have led to a so-called credibility crisis. The answer from the scientific community has been an increased focus on implementing reproducible research in the computational sciences. Researchers and scientists have addressed this increasingly important problem by proposing best practices as well as making available tools for aiding in implementing them. We discuss and give an example of how to implement such best practices using scientific Python packages. Our focus is on how to store the relevant metadata along with the results of a computational experiment. We propose the use of JSON and the HDF5 database and detail a reference implementation in the Magni Python package. Further, we discuss the focuses and purposes of the broad range of available tools for making scientific computations reproducible. We pinpoint the particular use cases that we believe are better solved by storing metadata along with results the same HDF5 database. Storing metadata along with results is important in implementing reproducible research and it is readily achievable using scientific Python packages.

Keywords

Reproducibility, Computational Science, HDF5

Bibtex entry

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