Outreach for Workflow Run RO-Crate

Please help us expand this list by letting us know if you have published/used/presented Workflow Run RO-Crate!

Cite us

Cite Workflow Run RO-Crate

Simone Leo, Michael R. Crusoe, Laura Rodríguez-Navas, Raül Sirvent, Alexander Kanitz, Paul De Geest, Rudolf Wittner, Luca Pireddu, Daniel Garijo, José M. Fernández, Iacopo Colonnelli, Matej Gallo, Tazro Ohta, Hirotaka Suetake, Salvador Capella-Gutierrez, Renske de Wit, Bruno P. Kinoshita, Stian Soiland-Reyes (2024):
Recording provenance of workflow runs with RO-Crate.
PLoS ONE 19(9):e0309210 https://doi.org/10.1371/journal.pone.0309210

Cite RO-Crate

Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble (2022): Packaging research artefacts with RO-Crate.
Data Science 5(2)
https://doi.org/10.3233/DS-210053

Cite WRROC profiles

To cite a particular Workflow Run RO-Crate profile, use its https://w3id.org/ persistent identifier (Permalink) or a citation using the Zenodo DOI:

Workflow Run RO-Crate working group (2024):
Process Run Crate specification. Version 0.5
Zenodo
https://w3id.org/ro/wfrun/process/0.5
https://doi.org/10.5281/zenodo.12158562

Workflow Run RO-Crate working group (2024):
Workflow Run Crate specification. Version 0.5
Zenodo
https://w3id.org/ro/wfrun/workflow/0.5
https://doi.org/10.5281/zenodo.12159311

Workflow Run RO-Crate working group (2024):
Provenance Run Crate specification. Version 0.5
Zenodo
https://w3id.org/ro/wfrun/provenance/0.5
https://doi.org/10.5281/zenodo.12160782

Publications

2025

Sean Wilkinson, Meznah Aloqalaa, Khalid Belhajjame, Michael R. Crusoe, Bruno de Paula Kinoshita, Luiz Gadelha, Daniel Garijo, Ove Johan Ragnar Gustafsson, Nick Juty, Sehrish Kanwal, Farah Zaib Khan, Johannes Köster, Karsten Peters-von Gehlen, Line Pouchard, Randy K. Rannow, Stian Soiland-Reyes, Nicola Soranzo, Shoaib Sufi, Ziheng Sun, Baiba Vilne, Merridee A. Wouters, Denis Yuen, Carole Goble (2025):
Applying the FAIR Principles to Computational Workflows.
Scientific Data 12:328 https://doi.org/10.1038/s41597-025-04451-9

Stian Soiland-Reyes, Stuart Wheater, Thomas Giles, Jonathan Couldridge, Phil Quinlan, Carole Goble (2025):
Five Safes RO-Crate: FAIR Digital Objects for Trusted Research Environments.
International FAIR Digital Objects Implementation Summit 2024, Berlin, Germany, 2024-03-20/–21.
Open Conference Proceedings *5
https://doi.org/10.52825/ocp.v5i.1419

Bruno de Paula Kinoshita, Edgar Garriga Nogales, Manuel Giménez de Castro Marciani, Miguel Castrillo Melguizo (2024):
FAIR Digital Objects in Autosubmit Workflows.
International FAIR Digital Objects Implementation Summit 2024, Berlin, Germany, 2024-03-20/–21.
Open Conference Proceedings *5
https://doi.org/10.52825/ocp.v5i.1416

Ove Johan Ragnar Gustafsson, Sean R. Wilkinson, Finn Bacall, Stian Soiland-Reyes, Simone Leo, Luca Pireddu, Stuart Owen, Nick Juty, José Mª Fernández, Tom Brown, Hervé Ménager, Björn Grüning, Salvador Capella-Gutierrez, Frederik Coppens, Carole Goble (2025):
WorkflowHub: a registry for computational workflows.
Scientific Data 12:837
https://doi.org/10.1038/s41597-025-04786-3

Paula Iborra, José M. Fernández, Laia Codo, Eugenio Gonzalo, Alexander Hambley, Stian Soiland-Reyes, Jonathan Couldridge, Carole Goble, Philip Quinlan, Salvador Capella-Gutierrez (2025):
ENTRUSTing WfExS 1.0 with WES and TES. (Poster)
ELIXIR All Hands Meeting 2025
https://doi.org/10.7490/f1000research.1120178.1

Polina Shpilker, Line Pouchard (2025):
Automatic Metadata Capture and Processing for High-Performance Workflows.
arXiv:2506.15537 [cs.DC]
https://doi.org/10.48550/arXiv.2506.15537

Mouna El Garb, Emmanuel Coquery, Fabien Duchateau, and Nicolas Lumineau (2025):
Improving reproducibility in bioinformatics workflows with BioFlow-Model.
2025 ACM Conference on Reproducibility and Replicability (under revision)
[preprint]

H. Omidi, L. Sacco, V. Hutter, G. Irsiegler, M. Claus, M. Schobben, A. Jacob, M. Schramm, S. Fiore (2025): Towards Provenance-Aware Earth Observation Workflows: the openEO Case Study
IEEE eScience 2025
[arXiv:2506.08597]

Sean R. Wilkinson, Johan Gustafsson, Finn Bacall, Khalid Belhajjame, Salvador Capella, Jose Maria Fernandez Gonzalez, Jacob Fosso Tande, Luiz Gadelha, Daniel Garijo, Patricia Grubel, Bjorn Grüning, Farah Zaib Khan, Sehrish Kanwal, Simone Leo, Stuart Owen, Luca Pireddu, Line Pouchard, Laura Rodríguez-Navas, Beatriz Serrano-Solano, Stian Soiland-Reyes, Baiba Vilne, Alan Williams, Merridee Ann Wouters, Frederik Coppens, Carole Goble (2025):
An Ecosystem of Services for FAIR Computational Workflows.
Book chapter, draft
arXiv 2505.15988 [cs.DC] https://doi.org/10.48550/arXiv.2505.15988

Irene Celino, Mario Scrocca, Agnese Chiatti (2025):
Mutual Understanding between People and Systems via Neurosymbolic AI and Knowledge Graphs.
Handbook on Neurosymbolic AI and Knowledge Graphs
Frontiers in Artificial Intelligence and Applications 400
https://doi.org/10.3233/FAIA250241 [arXiv:2504.11200]

Chris Card, Rachel Heaven, Andrew Kingdon, Patrick Bell, Alex Baldwin, Jeremy Carter, Jonathan Coney, Jonathan Cooper, Itahisa Gonzalez Alvarez, Michael Hollaway, Matthew McCormack, David Poulter, Ag Stephens, Philip Trembath (2025):
Publishing Environmental Data APIs for use in AI workflows: recommendations and demonstrators of a standard approach within the NERC Environmental Data Service.
NERC (OR/25/045)
https://nora.nerc.ac.uk/id/eprint/539708

Gabriele Padovani, Valentine Anantharaj, Sandro Fiore (2025):
Provenance Tracking in Large-Scale Machine Learning Systems.
arXiv:2507.01075 [cs.LG]
https://doi.org/10.48550/arXiv.2507.01075

Raül Sirvent, Rocío Carratalá-Saez, Amal Gueroudji, Tanzima Islam, Line Pouchard, Michela Taufer (2025):
Reproducibility for HPC and Distributed Environments:Committees, Nondeterminism, Performance, and Workflows.
Proceedings of 2025 ACM Conference on Reproducibility and Replicability (ACM REP’25). (in print)

2024

Mahnoor Zulfiqar, Michael R. Crusoe, Birgitta König-Ries, Christoph Steinbeck,Kristian Peters Luiz Gadelha (2024): Implementation of FAIR Practices in Computational Metabolomics Workflows—A Case Study. Metabolites 14(2) https://doi.org/10.3390/metabo14020118

David Bouyssié, Pınar Altıner, Salvador Capella-Gutierrez, José M. Fernández, Yanick Paco Hagemeijer, Peter Horvatovich, Martin Hubálek, Fredrik Levander, Pierluigi Mauri, Magnus Palmblad, Wolfgang Raffelsberger, Laura Rodríguez-Navas, Dario Di Silvestre, Balázs Tibor Kunkli, Julian Uszkoreit, Yves Vandenbrouck, Juan Antonio Vizcaíno, Dirk Winkelhardt, Veit Schwämmle (2024):
WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows.
Journal of Proteome Research 23(1)
https://doi.org/10.1021/acs.jproteome.3c00636

The Galaxy Community (2024):
*The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update.
Nucleic Acids Research 52(W1)
https://doi.org/10.1093/nar/gkae410

Pablo Orviz, Daniele Lezzi, Miguel Caballer, Michele Carpenè, Mario David, Samuel Bernardo, Raül Sirvent, DT-GEO (2024):
DT-GEO Deliverable: D2.2 DT-GEO Interfaces and 1st Software Release.
Digital.CSIC https://doi.org/10.20350/digitalCSIC/16578

Keith Jeffery, Pablo Orviz, DT-GEO (2024):
DT-GEO Deliverable: D4.1 Requirement analysis for the architecture of the assets supply.
Digital.CSIC https://doi.org/10.20350/digitalCSIC/16580

Keith Jeffery, Pablo Orviz, Rossana Paciello, DT-GEO (2024):
DT-GEO Deliverable: D2.4 Metadata Description of the Workflow Components.
Digital.CSIC https://doi.org/10.20350/digitalCSIC/17054

Eleni Adamidi, Panagiotis Deligiannis, Aikaterina Mastoraki, Thanasis Vergoulis (2024):
Proposing a New RO-Crate Profile for Enhanced Reproducibility in Computational Experiments.
_ 8th World Conference on Research Integrity (WCRI 2024)_, Athens
https://doi.org/10.5281/zenodo.11200097

Ludovica Sacco, Carolina Sopranzetti, Sandro Fiore (2024):
Enabling Provenance Tracking in Workflow Management Systems.
2024 IEEE International Conference on Big Data (BigData)
https://doi.org/10.1109/BigData62323.2024.10825405 (no preprint available?)

Alexander Rogers, Famke Bäuerle, Martin Beracochea, Alireza Heidari, Matt Burridge, Benedikt Osterholz, Alexander Sczyrba, Mahfouz Shehu, Tom Tubbesing, Anil Wipat (2024):
Enhancing multi-omic analyses through a federated microbiome analysis service.
BioHackrXiv
https://doi.org/10.37044/osf.io/3x274

José María Fernández González, Paula Iborra, Sebastien Moretti, Arun Isaac, Paul De Geest, Stian Soiland-Reyes (2024):
BioHackEU23: FAIR Workflow Execution with WfExS and Workflow Run Crate.
BioHackrXiv
https://doi.org/10.37044/osf.io/7f94w

Stian Soiland-Reyes, Eli Chadwick, Finn Bacall, José Mª Fernández, Björn Grüning, Hakan Bayındır (2024):
EuroScienceGateway D2.1: Reproducible FAIR Digital Objects for Workflows. (project deliverable)
Zenodo
https://doi.org/10.5281/zenodo.13225792

Stian Soiland-Reyes, Eli Chadwick,, Armin Dadras, Björn Grüning, Catalin Condurache, Sebastian Luna-Valero, Volodymyr Savchenko (2025):
EuroScienceGateway D2.2: Publishing workflow enriched FDOs to EOSC. (project deliverable)
Zenodo https://doi.org/10.5281/zenodo.15094824

Bruno De Paula Kinoshita, Daniel Beltran Mora, Manuel G. Marciani, Luiggi Tenorio Ku (2024):
Workflow Provenance with RO-Crate in Autosubmit.
EGU General Assembly 2024
https://doi.org/10.5194/egusphere-egu24-20642

2023

Simone Leo, Michael R. Crusoe, Laura Rodríguez-Navas, Raül Sirvent, Alexander Kanitz, Paul De Geest, Rudolf Wittner, Luca Pireddu, Daniel Garijo, José M. Fernández, Iacopo Colonnelli, Matej Gallo, Tazro Ohta, Hirotaka Suetake, Salvador Capella-Gutierrez, Renske de Wit, Bruno de Paula Kinoshita, Stian Soiland-Reyes (2023): Recording provenance of workflow runs with RO-Crate. arXiv:2312.07852 https://doi.org/10.48550/arXiv.2312.07852

Ignacio Eguinoa, Marek Suchánek, Vojtěch Knaisl, Jan Slifka, Paul De Geest, David López, Bjorn Gruning, Simone Leo, Stian Soiland-Reyes (2023):
BioHackEU22 Report: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates.
BioHackrXiv
https://doi.org/10.37044/osf.io/24jst

José M. Fernández, Laura Rodriguez-Navas, Salvador Capella-Gutiérrez (2023): WfExS-backend in the WRROC world?.
ELIXIR All Hands meeting 2023 (poster), Dublin, Ireland, 2023-06-05/–08
F1000Research 12(ELIXIR):616 (poster)
https://doi.org/10.7490/f1000research.1119457.1

Simone Leo, Laura Rodríguez-Navas, José M. Fernández, Paul De Geest, Luca Pireddu, Michael R. Crusoe, Daniel Garijo, Iacopo Colonnelli, Raül Sirvent, Stian Soiland-Reyes (2023): Making workflow provenance FAIR across workflow systems with Workflow Run RO-Crate.
ELIXIR All Hands meeting 2023 (poster), Dublin, Ireland, 2023-06-05/–08
F100Research 12(ELIXIR):592 (poster)
https://doi.org/10.7490/f1000research.1119445.1BioHackEU23

Simone Leo (2023):
RO-Crate for workflow run provenance.
CWL Conference 2023, 2023-02-27
[video (YouTube)] [video (ConfTube)] [slides]

Hirotaka Suetake, Tsukasa Fukusato, Takeo Igarashi, Tazro Ohta (2023):
A workflow reproducibility scale for automatic validation of biological interpretation results.
GigaScience 12:giad031
https://doi.org/10.1093/gigascience/giad031

2022

Paul De Geest, Frederik Coppens, Stian Soiland-Reyes, Ignacio Eguinoa, Simone Leo (2022):
Enhancing RDM in Galaxy by integrating RO-Crate.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster) Research Ideas and Outcomes 8:e95164
https://doi.org/10.3897/rio.8.e95164

Alex Hardisty, Paul Brack, Carole Goble, Laurence Livermore, Ben Scott, Quentin Groom, Stuart Owen, Stian Soiland-Reyes (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) https://doi.org/10.1162/dint_a_00134

Florence Bietrix, José Maria Carazo, Salvador Capella-Gutierrez, Frederik Coppens, Maria Luisa Chiusano, Romain David, Jose Maria Fernandez, Maddalena Fratelli, Jean-Karim Heriche, Carole Goble, Philip Gribbon, Petr Holub, Robbie P. Joosten, Simone Leo, Stuart Owen, Helen Parkinson, Roland Pieruschka, Luca Pireddu, Luca Porcu, Michael Raess, Laura Rodriguez-Navas, Andreas Scherer, Stian Soiland-Reyes, Jing Tang, Gary Saunders (2022):
EOSC-Life Methodology framework to enhance reproducibility within EOSC-Life – revised version.
Zenodo, EOSC-Life project deliverable
https://doi.org/10.5281/zenodo.7137743

Raül Sirvent, Javier Conejero, Francesc Lordan, Jorge Ejarque, Laura Rodríguez-Navas, José M. Fernández (2022):
Automatic, Efficient and Scalable Provenance Registration for FAIR HPC Workflows.
2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS)
https://doi.org/10.1109/WORKS56498.2022.00006