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Open-source Data Processing in Stable Isotope Ratio Mass Spectrometry: New Software Packages for Efficient, Transparent and Reproducible IRMS Data Reduction
  • Sebastian Kopf
Sebastian Kopf
University of Colorado at Boulder

Corresponding Author:sebastian.kopf@colorado.edu

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The key to reproducible data reduction and data processing in scientific research is the ability to faithfully record every step of the process in a reproducible format that is transparent and easy to communicate. This is not an easy task. Most of the time in experimental research that is not primarily computational in nature, it falls victim to the enormous effort required to design experiments well, run complex analytical procedures rigorously and efficiently, and interpret the results in the proper geologic, geochemical or biological context, with little time left to invest in documenting and constructing a reproducible data reduction workflow. While this is understandable, it introduces a high risk for error, makes it extremely difficult to share and discuss one’s approach or review others’, reproduce the calculations at a later point or even just revisit what was done conceptually. Part of the problem lies inherently with most data processing being difficult to document, part of black box process where the inner workings are inaccessible, or simply too divorced from the narrative of the scientific work it represents. One important obstacle that interferes frequently with attempts to remedy this situation in the stable isotope community is the lack of many basic computational and data access tools that enable the kinds of calculations and data processing isotope geochemists need to do on a day to day basis. Here, we introduce a new suite of software packages that provide efficient and transparent access to raw stable isotope ratio mass spectrometry (IRMS) data formats and enable reproducible data processing straight from raw analytical output through data reduction, quality control, visualization and data reporting that retains the necessary flexibility required for the enormous breadth of analytical goals in the stable isotope community. Presented tools will cover aspects of functionality provided by the isoreader (isoreader.kopflab.org), isoviewer (isoviewer.kopflab.org) and isoprocessor (isoprocessor.kopflab.org) software packages and are 100% open-source and freely available to everyone in the geochemical community and beyond.