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Meznah Aloqalaa

Publications and source records attributed to Meznah Aloqalaa.

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PRIMAD-LID: A Developed Framework for Computational Reproducibility

Over the past decade alongside increased focus on computational reproducibility significant efforts have been made to define reproducibility. However, these definitions provide a textual description rather than a framework. The community has sought conceptual frameworks that identify all factors that must be controlled and described for credible computational reproducibility. The PRIMAD model was initially introduced to address inconsistencies in terminology surrounding computational reproducibility by outlining six key factors: P (Platforms), R (Research objective), I (Implementations), M (Methods), A (Actors), and D (Data). Subsequently various studies across different fields adopted the model and proposed extensions. However, these contributions remain fragmented and require systematic integration and cross-disciplinary validation. To bridge this gap and recognising that PRIMAD provides a broadly applicable framework for reproducibility in computational science, this work undertakes a focused investigation of the PRIMAD model. It combines the models previous extensions into a unified framework suitable for diverse research contexts. The result is PRIMAD-LID, a discipline-diagnostic reproducibility framework that retains the original six PRIMAD dimensions and enhances each with three overarching modifiers: Lifespan (temporal qualifier), Interpretation (contextual reasoning) and Depth (necessary granularity), thereby establishing a more cohesive and robust foundation for computational reproducibility practices.

cs.CE

Applying the FAIR Principles to computational workflows

Recent trends within computational and data sciences show an increasing recognition and adoption of computational workflows as tools for productivity and reproducibility that also democratize access to platforms and processing know-how. As digital objects to be shared, discovered, and reused, computational workflows benefit from the FAIR principles, which stand for Findable, Accessible, Interoperable, and Reusable. The Workflows Community Initiative's FAIR Workflows Working Group (WCI-FW), a global and open community of researchers and developers working with computational workflows across disciplines and domains, has systematically addressed the application of both FAIR data and software principles to computational workflows. We present recommendations with commentary that reflects our discussions and justifies our choices and adaptations. These are offered to workflow users and authors, workflow management system developers, and providers of workflow services as guidelines for adoption and fodder for discussion. The FAIR recommendations for workflows that we propose in this paper will maximize their value as research assets and facilitate their adoption by the wider community.

cs.DL

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

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. This study, along with its artifacts, is reported as a RO-Crate, providing a structured reporting approach, which is available at https://doi.org/10.5281/zenodo.14317922.

cs.CE