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References

  1. Ian Walsh, Dmytro Fishman, Dario Garcia-Gasulla, Tiina Titma, Gianluca Pollastri, ELIXIR Machine Learning Focus Group, Jennifer Harrow, Fotis E. Psomopoulos, and Silvio C. E. Tosatto. DOME: recommendations for supervised machine learning validation in biology. Nature Methods, 18(10):1122–1127, 2021. doi:10.1038/s41592-021-01205-4. ↩

  2. Omar Abdelghani Attafi, Davide Cirillo, Alexander Miguel Monzon, Maria Chatzou Dunford, Gavin Farrell, Jennifer Harrow, Fotis E. Psomopoulos, and Silvio C. E. Tosatto. DOME registry: implementing community-wide recommendations for reporting supervised machine learning in biology. GigaScience, 13:giae094, 2024. doi:10.1093/gigascience/giae094. ↩

  3. Gavin Farrell, Omar Abdelghani Attafi, Styliani-Christina Fragkouli, Ignacio Heredia, Saul Fernández Tobías, Melissa Harrison, Henning Hermjakob, Matt Jeffryes, Marta Obregón Ruiz, Matt Pearce, Nikos Pechlivanis, Alvaro López García, Fotis Psomopoulos, and Silvio C. E. Tosatto. DOME copilot: making transparency and reproducibility for artificial intelligence methods simple. bioRxiv, 2026. Preprint, posted 19 April 2026. doi:10.64898/2026.04.16.718888. ↩

  4. Gavin Farrell, Eleni Adamidi, Rafael Andrade Buono, Mihail Anton, Omar Abdelghani Attafi, Salvador Capella Gutierrez, Emidio Capriotti, Leyla Jael Castro, Davide Cirillo, Fotis Psomopoulos, Silvio C. E. Tosatto, and others. Open and sustainable AI: challenges, opportunities and the road ahead in the life sciences. Nature Methods, 2026. doi:10.1038/s41592-026-03037-6. ↩

  5. Gavin Farrell, Eleni Adamidi, Rafael Andrade Buono, and others. Open and sustainable AI: challenges, opportunities and the road ahead in the life sciences. arXiv preprint, 2025. doi:10.48550/arXiv.2505.16619. ↩

  6. Geert van Geest, Elin Kronander, Jose Alejandro Romero Herrera, Nace Žlender, ELIXIR Training Coordination Team, and Alexandra Cardona. ELIXIR training lesson template. 2023. doi:10.5281/zenodo.7913092. ↩

  7. OSAI Ecosystem Contributors and ELIXIR Machine Learning Focus Group. OSAI: open and sustainable AI ecosystem components list. 2025. doi:10.5281/zenodo.15391274. ↩

  8. BioComputingUP. Dome-schema: the versioned DOME registry data model. 2026. URL: https://github.com/BioComputingUP/dome-schema. ↩

  9. Gavin Farrell. DOME agent skill. 2026. Licensed CC BY 4.0. URL: https://github.com/gavinf97/dome-agent-skill. ↩