Join or align with a community effort

Join, or align with, a community that is related to your software type or language. Their standards and guidelines will often help make your software findable and citable.

How?

Using a Nextflow computational workflow as an example, there are effectively three levels of community involvement:

1. Just adopting Nextflow, as it is a popular and well maintained workflow language.
2. Following community defined (i.e. nf-core) workflow development best practices.
3. Joining the nf-core community and contributing a workflow directly to their existing maintained collection.

Examples

• R: Visit Bioconductor (Huber et al., 2015)
• Python: Visit the community page to learn more
• BioContainers (Da Veiga Leprevost et al., 2017)
• CWL: Visit this community effort focused on developing CWL workflows
• Galaxy Project: The Galaxy project has many communities that address software. The most prominent include:
  • Intergalactic Utilities Commission (IUC): software
  • Intergalactic Workflows Commission (IWC): computational workflows
  • There are also many domain specific communities as well, including for example, microGalaxy community and Galaxy Proteomics (Galaxy-P) (Sheynkman et al., 2014).
• Nextflow: nf-core (Ewels et al., 2020) is a significant effort in this space, and there are talks, training and hackathons you can join. Check out their join nf-core page to find out how to get involved.
• Snakemake (Mölder et al., 2021): Visit this community effort focused on developing Snakemake workflows and don’t forget to check the different ways you can get support.

A selection of community guidelines and standards for software

References

1. Huber, W., Carey, V. J., Gentleman, R., Anders, S., Carlson, M., Carvalho, B. S., Bravo, H. C., Davis, S., Gatto, L., Girke, T., Gottardo, R., Hahne, F., Hansen, K. D., Irizarry, R. A., Lawrence, M., Love, M. I., MacDonald, J., Obenchain, V., Oleś, A. K., … Morgan, M. (2015). Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods, 12(2), 115–121. https://doi.org/10.1038/nmeth.3252
2. Da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics, 33(16), 2580–2582. https://doi.org/10.1093/bioinformatics/btx192
3. Sheynkman, G. M., Johnson, J. E., Jagtap, P. D., Shortreed, M. R., Onsongo, G., Frey, B. L., Griffin, T. J., & Smith, L. M. (2014). Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations. BMC Genomics, 15(1), 703. https://doi.org/10.1186/1471-2164-15-703
4. Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276–278. https://doi.org/10.1038/s41587-020-0439-x
5. Mölder, F., Jablonski, K. P., Letcher, B., Hall, M. B., Tomkins-Tinch, C. H., Sochat, V., Forster, J., Lee, S., Twardziok, S. O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., Nahnsen, S., & Köster, J. (2021). Sustainable data analysis with Snakemake. F1000Research, 10, 33. https://doi.org/10.12688/f1000research.29032.1
6. Barker, M., Chue Hong, N. P., Katz, D. S., Lamprecht, A.-L., Martinez-Ortiz, C., Psomopoulos, F., Harrow, J., Castro, L. J., Gruenpeter, M., Martinez, P. A., & Honeyman, T. (2022). Introducing the FAIR Principles for research software. Scientific Data, 9(1), 622. https://doi.org/10.1038/s41597-022-01710-x
7. Alves, R., Bampalikis, D., Castro, L. J., Fernández, J. M., Harrow, J., Kuzak, M., Martin, E., Psomopoulos, F. E., & Via, A. (2021). ELIXIR Software Management Plan for Life Sciences [Preprint]. BioHackrXiv. https://doi.org/10.37044/osf.io/k8znb

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