Open-Source Codes

The reproducibility or replication “crisis” in science has garnered considerable attention in both the scientific 1 and popular press 2, and in Congress 3. Reproducibility is one of the foundations of science. The recent move towards open science, where raw data and codes are made publicly available, provides a means to improve reproducibility; if you cannot see the raw data and if you cannot see exactly how data was analyzed or simulated, it is impossible to reproduce the results. The Innovative Concepts Group, which is committed to open science, has developed and made publicly available several data analysis codes, and collaborates with the Flash Center on the development of the open-source MHD code FLASH. Data analysis codes that are currently available include:
Thomson scattering and charged particle radiography routines in PlasmaPy http://doi.org/10.5281/zenodo.4602818
Fiducia: cubic spline fitting for filtered diode arrays https://pypi.org/project/fiducia/
Self-optimizing Savitzky-Golay filter for generalized signal denoising https://github.com/Plasmacaster/Optimized_SavGol
A 2-D electrostatic PIC code for direct inversion of deflectometry data (Version 3). Zenodo. https://doi.org/10.5281/zenodo.6638811
A Matlab function to solve the Monge-Ampere equation using the Sulman, Williams and Russell algorithm, (Version 1). Zenodo. https://doi.org/10.5281/zenodo.6685314

1 M. Baker, Nature 533, 452 (2016); T. Miyakawa, Mol. Brain 13, 24 (2020).

2 J. Lehrer, The New Yorker, 5 December 2010; J. Whitfield, Replication Crisis, Comments on Science Fictions: Exposing Fraud, Bias, Negligence and Hype in Science by Stuart Richie, Vol. 43 (LRB, London, 2021).

3 Reproducibility and Replicability in Science, National Academies of Sciences, Engineering, Medicine (The National Academies Press, Washington, DC, 2019).