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ZENODO
Dataset . 2024
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2024
License: CC BY
Data sources: Datacite
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Systematically Examining Reproducibility: A Case Study for High Throughput Sequencing using the PRIMAD Model and BioCompute Object

Authors: Aloqalaa, Meznah; Soiland-Reyes, Stian; Goble, Carole;

Systematically Examining Reproducibility: A Case Study for High Throughput Sequencing using the PRIMAD Model and BioCompute Object

Abstract

The reproducibility of computational pipelines is an expectation in biomedical science, particularly in critical domains like human health. In this context, reporting next-generation genome sequencing methods used in precision medicine spurred the development of the IEEE 2791-2020 standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS), known as the BioCompute Object (BCO). Championed by the USA’s Food and Drug Administration, the BCO is a pragmatic framework for documenting pipelines; however, it has not been systematically assessed for its reproducibility claims. This study uses the PRIMAD model, a conceptual framework for describing computational experiments for reproducibility purposes, to systematically review the BCO for depth and coverage. A meticulous mapping of BCO and PRIMAD elements onto a published BCO use case reveals potential omissions and necessary extensions within both frameworks. This underscores the significance of systematically validating claims of reproducibility for published digital objects, thereby enhancing the reliability of scientific research in bioscience and related disciplines. The associated publication for this study can be found on arXiv at: http://arxiv.org/abs/2412.07502 This study, along with its associated artifacts, is reported as a RO-Crate, providing a structured reporting approach.

Related Organizations
Keywords

BioCompute Object, PRIMAD Model, Computational science, Reproducibility, Computational Reproducibility

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average