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S. (Stian) Soiland-Reyes

PhD Candidate
Faculty of Science
Informatics Institute

  • Research and publications
  • Publications

    2022

    • Soiland-Reyes, S., Bayarri, G., Andrio, P., Long, R., Lowe, D., Niewielska, A., Hospital, A., & Groth, P. (2022). Making Canonical Workflow Building Blocks interoperable across workflow languages. Data Intelligence, 4(2), Article 342–357. https://doi.org/10.5281/zenodo.5727730, https://doi.org/10.1162/dint_a_00135 [details]
    • Soiland-Reyes, S., Sefton, P., Crosas, M., Castro, L. J., Coppens, F., Fernández, J. M., Garijo, D., Grüning, B., La Rosa, M., Leo, S., Ó Carragáin, E., Portier, M., Trisovic, A., RO-Crate Community, Groth, P., & Goble, C. (2022). Packaging research artefacts with RO-Crate. Data Science, 5(2), 97-138. Advance online publication. https://doi.org/10.3233/DS-210053 [details]

    2023

    • David, R., BY-COVID project community, ISIDORe project community, Richard, A. S., Connellan, C., Lauer, K. B., Chiusano, M. L., Goble, C., Houde, M., Kemmer, I., Keppler, A., Lieutaud, P., Ohmann, C., Panagiotopoulou, M., Khan, S. R., Rybina, A., Soiland-Reyes, S., Wit, C., Wittner, R., ... Ewbank, J. (2023). Umbrella Data Management Plans to Integrate FAIR Data: Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness. Data Science Journal, 22, Article 35. https://doi.org/10.5334/dsj-2023-035
    • Meurisse, M., Estupiñán-Romero, F., González-Galindo, J., Martínez-Lizaga, N., Royo-Sierra, S., Saldner, S., Dolanski-Aghamanoukjan, L., Degelsegger-Marquez, A., Soiland-Reyes, S., Van Goethem, N., Bernal-Delgado, E., & BeYond-COVID project (2023). Federated causal inference based on real-world observational data sources: application to a SARS-CoV-2 vaccine effectiveness assessment. BMC Medical Research Methodology, 23, Article 248. https://doi.org/10.1186/s12874-023-02068-3 [details]

    2022

    • Brack, P., Crowther, P., Soiland-Reyes, S., Owen, S., Lowe, D., Williams, A. R., Groom, Q., Dillen, M., Coppens, F., Grüning, B., Eguinoa, I., Ewels, P., & Goble, C. (2022). Ten Simple Rules for making a software tool workflow-ready. PLoS Computational Biology, 18(3), Article e1009823. https://doi.org/10.5281/zenodo.5636487, https://doi.org/10.1371/journal.pcbi.1009823 [details]
    • Crusoe, M. R., Abeln, S., Iosup, A., Amstutz, P., Chilton, J., Tijanić, N., Ménager, H., Soiland-Reyes, S., Gavrilović, B., Goble, C. A., & CWL Community (2022). Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language. Communications of the ACM, 65(6), 54-63. Advance online publication. https://doi.org/10.1145/3486897 [details]
    • Hardisty, A., Brack, P., Goble, C., Livermore, L., Scott, B., Groom, Q., Owen, S., & Soiland-Reyes, S. (2022). The Specimen Data Refinery: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections. Data Intelligence, 4(2), 320–341. https://doi.org/10.1162/dint_a_00134 [details]
    • Soiland-Reyes, S., Bayarri, G., Andrio, P., Long, R., Lowe, D., Niewielska, A., Hospital, A., & Groth, P. (2022). Making Canonical Workflow Building Blocks interoperable across workflow languages. Data Intelligence, 4(2), Article 342–357. https://doi.org/10.5281/zenodo.5727730, https://doi.org/10.1162/dint_a_00135 [details]
    • Soiland-Reyes, S., Sefton, P., Crosas, M., Castro, L. J., Coppens, F., Fernández, J. M., Garijo, D., Grüning, B., La Rosa, M., Leo, S., Ó Carragáin, E., Portier, M., Trisovic, A., RO-Crate Community, Groth, P., & Goble, C. (2022). Packaging research artefacts with RO-Crate. Data Science, 5(2), 97-138. Advance online publication. https://doi.org/10.3233/DS-210053 [details]

    2021

    • Ferreira da Silva, R., Casanova, H., Chard, K., Altintas, I., Badia, R. M., Balis, B., Coleman, T., Coppens, F., Di Natale, F., Enders, B., Fahringer, T., Filgueira, R., Fursin, G., Garijo, D., Goble, C., Howell, D., Jha, S., Katz, D. S., Laney, D., ... Wolf, M. (2021). A Community Roadmap for Scientific Workflows Research and Development. In 2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS 2021): St. Louis, Missouri, USA, 15 November 2021 (pp. 81-90). IEEE. https://doi.org/10.1109/WORKS54523.2021.00016 [details]
    • Kuhn, T., Taelman, R., Emonet, V., Antonatos, H., Soiland-Reyes, S., & Dumontier, M. (2021). Semantic micro-contributions with decentralized nanopublication services. PeerJ Computer Science, 7, Article e387. https://doi.org/10.7717/peerj-cs.387 [details]
    • Lamprecht, A.-L., Palmblad, M., Ison, J., Schwämmle, V., Al Manir, M. S., Altintas, I., Baker, C. J. O., Ben Hadj Amor, A., Capella-Gutierrez, S., Charonyktakis, P., Crusoe, M. R., Gil, Y., Goble, C., Griffin, T. J., Groth, P., Ienasescu, H., Jagtap, P., Kalaš, M., Kasalica, V., ... Wolstencroft, K. (2021). Perspectives on automated composition of workflows in the life sciences. F1000Research, 10, Article 897. https://doi.org/10.12688/f1000research.54159.1 [details]
    • Wittner, R., Holub, P., Müller, H., Geiger, J., Goble, C., Soiland-Reyes, S., Pireddu, L., Frexia, F., Mascia, C., Fairweather, E., Swedlow, J. R., Moore, J., Strambio, C., Grunwald, D., & Nakae, H. (2021). ISO 23494: Biotechnology – Provenance Information Model for Biological Specimen And Data. In B. Glavic, V. Braganholo, & D. Koop (Eds.), Provenance and Annotation of Data and Processes: 8th and 9th International Provenance and Annotation Workshop, IPAW 2020 + IPAW 2021, virtual event, July 19–22, 2021 : proceedings (pp. 222-225). (Lecture Notes in Computer Science; Vol. 12839). Springer. https://doi.org/10.5281/zenodo.5004842, https://doi.org/10.1007/978-3-030-80960-7_16 [details]

    2024

    • Wittner, R., Holub, P., Mascia, C., Frexia, F., Müller, H., Plass, M., Allocca, C., Betsou, F., Burdett, T., Cancio, I., Chapman, A., Chapman, M., Courtot, M., Curcin, V., Eder, J., Elliot, M., Exter, K., Goble, C., Golebiewski, M., ... Geiger, J. (2024). Toward a common standard for data and specimen provenance in life sciences. Learning Health Systems, 8(1), Article e10365. https://doi.org/10.1002/lrh2.10365 [details]

    2023

    2022

    • Arend, D., Beier, S., Bouri, L., Brandizi, M., Hobern, D., Le Floch, E., Mühlhaus, T., Pommier, C., Owen, S., Rocca-Serra, P., Rosnet, T., & Soiland-Reyes, S. (2022). BioHackEU22 Project 22: Plant data exchange and standard interoperability. BioHackrXiv. https://doi.org/10.37044/osf.io/c724r [details]
    • Geest, P. D., Coppens, F., Soiland-Reyes, S., Eguinoa, I., & Leo, S. (2022). Enhancing RDM in Galaxy by integrating RO-Crate. Research Ideas and Outcomes, 8, Article e95164. https://doi.org/10.3897/rio.8.e95164
    • Soiland-Reyes, S., Castro, L. J., Garijo, D., Portier, M., Goble, C., & Groth, P. (2022). Updating Linked Data practices for FAIR Digital Object principles. Research Ideas and Outcomes, 8, Article e94501. https://doi.org/10.3897/rio.8.e94501
    • Soiland-Reyes, S., Sefton, P., Castro, L. J., Coppens, F., Garijo, D., Leo, S., Portier, M., & Groth, P. (2022). Creating lightweight FAIR Digital Objects with RO-Crate. Research Ideas and Outcomes, 8, Article e93937. https://doi.org/10.3897/rio.8.e93937
    • Woolland, O., Brack, P., Soiland-Reyes, S., Scott, B., & Livermore, L. (2022). Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows. Research Ideas and Outcomes, 8, Article e94349. https://doi.org/10.3897/rio.8.e94349

    2021

    • Holub, P., Wittner, R., Mascia, C., Frexia, F., Müller, H., Plass, M., Allocca, C., Betsou, F., Burdett, T., Cancio, I., Chapman, A., Chapman, M., Courtot, M., Curcin, V., Eder, J., Elliot, M., Exter, K., Fairweather, E., Goble, C., ... Geiger, J. (2021). Towards a Common Standard for Data and Specimen Provenance in Life Sciences. (v1 ed.) Zenodo. https://doi.org/10.5281/zenodo.5093125 [details]

    2022

    • Soiland-Reyes, S., Sefton, P., Castro, L. J., Coppens, F., Garijo, D., Leo, S., Portier, M., Groth, P., & Goble, C. (2022). Creating lightweight FAIR Digital Objects with RO-Crate and FAIR Signposting. Poster session presented at 1st International Conference on FAIR Digital Objects , Leiden, Netherlands. https://doi.org/10.5281/zenodo.7245315
    • Woolland, O., Brack, P., Soiland-Reyes, S., Scott, B., & Livermore, L. (2022). Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows. Poster session presented at 1st International Conference on FAIR Digital Objects , Leiden, Netherlands. https://doi.org/10.5281/zenodo.7233688

    Membership / relevant position

    Talk / presentation

    2021

    • Goble, C., Soiland-Reyes, S., Bacall, F., Owen, S., Williams, A., Eguinoa, I., Droesbeke, B., Leo, S., Pireddu, L., Rodríguez-Navas, L., Fernández, J. M., Capella-Gutierrez, S., Ménager, H., Grüning, B., Serrano-Solano, B., Ewels, P., & Coppens, F. (2021). Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory. (v1 ed.) Zenodo. https://doi.org/10.5281/zenodo.4605654 [details]

    2023

    2019

    This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications. Log in to Personal Page Publication Selection tool to manage the visibility of your publications on this list.
  • Ancillary activities
    No ancillary activities