Talk An exobiological illustration of the Org approach for Literate Programming and Reproducible Research

Abstract

Authors: Laurent Binet, Mathilde Bourbin, Mariem El Afrit, Didier Gourier, Yann Le Du

Presentation by Yann Le Du [i] and Mariem El Afrit [ii]
[i] yann@hpu4science.org
[ii] mariem@hpu4sciene.org

Abstract

Electron Paramagnetic Resonance (EPR) is a non-destructive, non-invasive technique useful for the characterization of organic moieties in carbonaceous matter that provides unique information in exobiology [1]. Usual EPR parameters are the peak-to-peak amplitude, the linewidth and the g factor; however, such parameters are not sufficient to fully describe a single EPR line. Combined to classic EPR parameters, we devised new constructive shape parameter that now allows a complete description of an EPR spectrum, and which turns out to be a very precise datation tool not only of carbonaceous matter, but also of any other substance characterized by a single symmetric EPR line.

With the benefit of our extensive experience with Python in scientific research [2], all of the data reduction, computations and analysis were done with Python and the Numpy and Cython extensions, but the real novelty lies in how we introduced a new methodology in the field of exobiology based on literate programming (LP) and reproducible research (RR): the whole study uses Sage [3], SageTeX [4], Org [5] and Babel [6]. The LP/RR methodology implies that the work consists in a master file and a few data-files that in themselves allows a complete understanding of the data reduction and analysis, and a full reproducibility given the raw data. We found this tight integration to be very efficient in convincing our exobiologist collaborators that the LP/RR paradigm was a very potent tool in their research. Thanks to this tight integration, the code can evolve easily and be adapted to new datasets or even transliterated in another language: each “code chunk” can exist in different languages and yield different complete programs. The result of this study will be published in a paper to be submitted to Open Research and Computation [7]. We would also like to share our workflow with the Scipy community: how we go from the Sage worksheet to the final Org LP/RR documents.

[1] Skrzypczak-Bonduelle, A and Binet, L and Delpoux, O and Vezin, H and Derenne, S and Robert, F and Gourier, D. EPR of radicals in primitive organic matter: A tool for the search of biosignatures of the most ancient traces of life. App Magn Reson - 2008

[2] http://hpu4science.org/

[3] http://www.sagemath.org/

[4] http://www.sagemath.org/fr/html/tutorial/sagetex.html

[5] http://orgmode.org/

[6] http://orgmode.org/worg/org-contrib/babel/

[7] http://www.openresearchcomputation.com/

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