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bioRxiv · 10.1101/2022.10.11.511695

A workflow reproducibility scale for automatic validation of biological interpretation results.

Suetake, H.·Fukusato, T.·Igarashi, T.·Ohta, T.
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Abstract

BackgroundReproducibility of data analysis workflow is a key issue in the field of bioinformatics. Recent computing technologies, such as virtualization, have made it possible to reproduce workflow execution with ease. However, the reproducibility of results is not well discussed; that is, there is no standard way to verify whether the biological interpretation of reproduced results are the same. Therefore, it still remains a challenge to automatically evaluate the reproducibility of results. ResultsWe propose a new metric, a reproducibility scale of workflow execution results, to evaluate the reproducibility of results. This metric is based on the idea of evaluating the reproducibility of results using biological feature values (e.g., number of reads, mapping rate, and variant frequency) representing their biological interpretation. We also implemented a prototype system that automatically evaluates the reproducibility of results using the proposed metric. To demonstrate our approach, we conducted an experiment using workflows used by researchers in real research projects and the use cases that are frequently encountered in the field of bioinformatics. ConclusionsOur approach enables automatic evaluation of the reproducibility of results using a fine-grained scale. By introducing our approach, it is possible to evolve from a binary view of whether the results are superficially identical or not to a more graduated view. We believe that our approach will contribute to more informed discussion on reproducibility in bioinformatics.

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Suetake, H., Fukusato, T., Igarashi, T., Ohta, T.. 2022-10-13. A workflow reproducibility scale for automatic validation of biological interpretation results.. https://doi.org/10.1101/2022.10.11.511695

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