Meeting Details
Date: 24-11-13
Time: 11:00-12:00
Location: Hybrid: Rm 6E032/34 and via Teams
Presenter: Dr. Wei Zhu
Building FAIR Bioinformatics Workflows: A Case Study Using De Novo Mutations Variant Calling in Snakemake
In modern genomics, ensuring that bioinformatics workflows adhere to FAIR principles (Findability, Accessibility, Interoperability, and Reusability), is critical for advancing research reproducibility and data sharing. This talk will explore the process of building FAIR bioinformatics workflows with a focus on variant calling for de novo mutations using Snakemake. We will show how Snakemake’s modular structure supports FAIR guidelines, and highlight the practical challenges and solutions involved in implementing FAIR bioinformatics workflows.
Articles for Discussion:
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de Visser, C., Johansson, L. F., Kulkarni, P., Mei, H., Neerincx, P., Joeri van der Velde, K., Horvatovich, P., van Gool, A. J., Swertz, M. A., Hoen, P. A. C. ’t, & Niehues, A. (2023). Ten quick tips for building FAIR workflows. PLoS Computational Biology, 19(9), e1011369. https://doi.org/10.1371/journal.pcbi.1011369
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Lamprecht, A.-L., Garcia, L., Kuzak, M., Martinez, C., Arcila, R., Martin Del Pico, E., Dominguez Del Angel, V., Van De Sandt, S., Ison, J., Martinez, P. A., & Others. (2020). Towards FAIR principles for research software. Brown University Digest of Addiction Theory and Application: DATA, 3(1), 37–59. https://content.iospress.com/articles/data-science/ds190026
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Goble, C., Cohen-Boulakia, S., Soiland-Reyes, S., Garijo, D., Gil, Y., Crusoe, M. R., Peters, K., & Schober, D. (2020). FAIR computational workflows. Data Intelligence, 2(1–2), 108–121. https://doi.org/10.1162/dint_a_00033
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Katz, D. S., Gruenpeter, M., & Honeyman, T. (2021). Taking a fresh look at FAIR for research software. Patterns (New York, N.Y.), 2(3), 100222. https://doi.org/10.1016/j.patter.2021.100222