Appendix C: Supplements

In addition to my main contributions, I have also been co-author on these articles during the PhD period, provided as supplements:

Supplement 1: Ten Simple Rules for making a software tool workflow-ready

Supplement 2: Enhancing RDM in Galaxy by integrating RO-Crate

Supplement 3: Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory Zenodo white paper

Supplement 4: Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

Supplement 5: Semantic micro-contributions with decentralized nanopublication services

Supplement 6: Perspectives on automated composition of workflows in the life sciences

Supplement 7: ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data

Supplement 8: Towards a Common Standard for Data and Specimen Provenance in Life Sciences

Supplement 9: A Community Roadmap for Scientific Workflows Research and Development

Supplement 10: Unique, Persistent, Resolvable: Identifiers as the Foundation of FAIR (Main contribution pre-dates UvA affiliation)

Supplement 11: FAIR Computational Workflows (Main contribution pre-dates UvA affiliation)

Supplement 12: Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv (Main contribution pre-dates UvA affiliation)

Supplement 13: IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication: IEEE Std 2791-2020

Supplement 14: BioHackEU22 Project 22: Plant data exchange and standard interoperability

Supplement 15: RO-Crate, a lightweight approach to Research Object data packaging (Main contribution pre-dates UvA affiliation)

Supplement 16: Federated causal inference based on real-world observational data sources: application to a SARS-CoV-2 vaccine effectiveness assessment

Supplement 17: Linking provenance and its metadata in multi-organizational environments of life sciences

Supplement 18: BioHackEU22 Report: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates

Supplement 19: BioHackEU23 report: Enabling continuous RDM using Annotated Research Contexts with RO-Crate profiles for ISA

Supplement 20: BioHackEU23 report: Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas

Supplement 21: Report on “FAIR Signposting” and its uptake by the community

Supplement 22: Practical webby FDOs with RO-Crate and FAIR Signposting: Experiences and lessons learned