Zenodo Data Sharing and Data Reuse User Story: Reusable Pipelines, Reproducible Insights: The Role of NUPulmonary/utils

This code repository can (and, to the best of our knowledge, does) help to guide researchers within Northwestern and throughout the research community in multi-omics data analysis as-is or through adaptation. Rogan A. Grant Reusable Pipelines, Reproducible Insights: The Role of NUPulmonary/utils Background As biomedical research increasingly relies on high-throughput sequencing and multi-omics data, the need for reproducible and standardized computational workflows has grown. The NUPulmonary/utils repository is a curated collection of R scripts and pipelines developed by the Northwestern Division of Pulmonary and Critical Care Medicine (PCCM) to support analyses in single-cell RNA sequencing, spatial transcriptomics, and immune profiling. Originally created in 2018, the repository has since supported a wide range of high-impact studies exploring mitochondrial function, immune signaling, and neuroinflammation. Its adoption across diverse biological contexts highlights how shared code can accelerate discovery, promote transparency, and uphold reproducibility in modern biomedical science. GREI data sharing and reuse story Published 2025-08-27 Researcher: Rogan A. Grant1 , et al Affiliation: 1: Northwestern University Software shared: NUPulmonary/utils/R Related publication: Multiple articles Funding: This work was supported by multiple grants from the National Institutes of Health, including R01, P01, U19, T32, F31, F32, K08, R35, and P30 mechanisms awarded to various investigators. Chandel Lab Research Team Evolution of Data Sharing Historically, data and code sharing in biology lacked clear standards and was applied inconsistently. With the rise of high-throughput and multi-omic techniques, publishing raw data and analysis code has become increasingly common and often expected. Platforms like SRA, GEO, and Zenodo now offer free, permanent storage, making reproducible research more accessible and sustainable across the field. Challenges and Solutions As data sharing practices in biology have evolved, researchers have encountered both technical and cultural challenges in making their work reproducible and accessible, including lack of permanent code archiving, and ensuring transparency during peer review. To address these challenges, the researchers: ● Archived the code on Zenodo, providing a DOI to ensure permanent, citable access. ● Made the repository publicly available, supporting reproducibility and enabling peer reviewers and readers to verify analyses. GREI Use Cases are supported by the National Institutes of Health (NIH) Office of Data Science Strategy/ Office of the NIH Director pursuant to OTA-21-009, “Generalist Repository Ecosystem Initiative (GREI)”. Impact of Data Sharing Sharing the NUPulmonary/utils repository has significantly enhanced the reproducibility and reach of pulmonary research. By making the code openly available, the PCCM Division enabled scientists to validate and extend its analyses across studies in COVID-19 immunology, neuroinflammation, and mitochondrial biology. Archiving the repository on Zenodo ensured long-term access and increased visibility, leading to citations in several high-impact publications. This demonstrates the value of open data in fostering transparency, collaboration, and scientific progress. Looking Forward As multi-omic research grows more complex, the need for accessible, well-documented code will only increase. Platforms like Zenodo will continue to complement GitHub by providing stable, citable archives that support transparency and reproducibility. The PCCM Division expects its shared codebase to remain a valuable resource for researchers and potentially contribute to future innovations, perhaps including AI-driven tools. Generalist Repository Ecosystem Initiative (GREI) Community https://zenodo.org/communities/grei/ Zenodo GREI Use Cases are supported by the National Institutes of Health (NIH) Office of Data Science Strategy/Office of the NIH Director pursuant to OTA-21-009, “Generalist Repository Ecosystem Initiative (GREI)” through through Other Transactions Agreement (OTA) Number 1OT2DB000013. Zenodo is an open-access repository developed by CERN through the OpenAIRE program. For over a decade, it has enabled researchers to share, preserve, and cite diverse research outputs. Powered by InvenioRDM, Zenodo offers a flexible, open-source foundation that supports modern research workflows and data management best practices. InvenioRDM is the engine and community behind Zenodo. 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Accelerating Research Sharing and Reuse with Zenodo and GREI Zenodo and GREI work collaboratively to support researchers in sharing, preserving, and reusing data across disciplines.