Outreach and Publications

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Cite WorkflowHub

If you would like to reference the WorkflowHub from academic work, please cite:

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 (2024):
WorkflowHub: a registry for computational workflows.
arXiv:2410.06941 [cs.DL]
https://doi.org/10.48550/arXiv.2410.06941

Recent publications, presentations, citations

2024

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 (2024):
Applying the FAIR Principles to Computational Workflows.
arXiv 2410.03490 [cs.DL]
https://doi.org/10.48550/arXiv.2410.03490

Nathan Maligeay, Noémie Bossut, Khalid Belhajjame (2024):
Why Do Scientific Workflows Still Break?
Proceedings of the 36th International Conference on Scientific and Statistical Database Management (SSDBM ‘24)
https://doi.org/10.1145/3676288.3676300

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

Scott Edmunds (2024):
A Decade of FAIR – and what next? Q&A on FAIR workflows with the Netherlands X-omics Initiative.
GIGAblog
http://gigasciencejournal.com/blog/fair-workflows/

Anna Niehues, Casper de Visser, Fiona A Hagenbeek, Purva Kulkarni, René Pool, Naama Karu, Alida S D Kindt, Gurnoor Singh, Robert R J M Vermeiren, Dorret I Boomsma, Jenny van Dongen, Peter A C ’t Hoen, Alain J van Gool (2024):
A multi-omics data analysis workflow packaged as a FAIR Digital Object.
GigaScience 13:giad115
https://doi.org/10.1093/gigascience/giad115

2023

Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodriguez-Navas, José M. Fernández, Björn Grüning, Simone Leo, Luca Pireddu, Michael Crusoe, Johan Gustafsson, Salvador Capella-Gutierrez, Frederik Coppens (2023):
The EOSC-Life Workflow Collaboratory for the Life Sciences.
Proceedings of the Conference on Research Data Infrastructure 1
https://doi.org/10.52825/cordi.v1i.352

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
https://doi.org/10.48550/arXiv.2312.07852

Romain David, Arina Rybina, Jean‐Marie Burel, Jean‐Karim Heriche, Pauline Audergon, Jan‐Willem Boiten, Frederik Coppens, Sara Crockett, Katrina Exter, Sven Fahrner, Maddalena Fratelli, Carole Goble, Philipp Gormanns, Tobias Grantner, Björn Grüning, Kim Tamara Gurwitz, John M Hancock, Henriette Harmse, Petr Holub, Nick Juty, Geoffrey Karnbach, Emma Karoune, Antje Keppler, Jessica Klemeier, Carla Lancelotti, Jean‐Luc Legras, Allyson L Lister, Dario Livio Longo, Rebecca Ludwig, Bénédicte Madon, Marzia Massimi, Vera Matser, Rafaele Matteoni, Michaela Th Mayrhofer, Christian Ohmann, Maria Panagiotopoulou, Helen Parkinson, Isabelle Perseil, Claudia Pfander, Roland Pieruschka, Michael Raess, Andreas Rauber, Audrey S Richard, Paolo Romano, Antonio Rosato, Alex Sánchez‐Pla, Susanna‐Assunta Sansone, Ugis Sarkans, Beatriz Serrano‐Solano, Jing Tang, Ziaurrehman Tanoli, Jonathan Tedds, Harald Wagener, Martin Weise, Hans V Westerhoff, Rudolf Wittner, Jonathan Ewbank, Niklas Blomberg, Philip Gribbon (2023):
“Be sustainable”: EOSC‐Life recommendatons for implementation of FAIR principles in life science data handling.
The EMBO Journal 42:e115008
https://doi.org/10.15252/embj.2023115008

Raül Sirvent (2023):
Workflow Provenance registration with COMPSs.
Innovative HPC workflows for industry, 2023-10-25, Munich, Germany
https://doi.org/10.5281/zenodo.10046567

Casper de Visser, Lennart F. Johansson, Purva Kulkarni, Hailiang Mei, Pieter Neerincx, K. Joeri van der Velde, Péter Horvatovich, Alain J. van Gool, Morris A. Swertz, Peter A. C. ‘t Hoen, Anna Niehues (2023):
Ten quick tips for building FAIR workflows.
PLOS Computational Biology 19(9): e1011369
https://doi.org/10.1371/journal.pcbi.1011369

Carole Goble, Stian Soiland-Reyes, Finn Bacall, Stuart Owen, Luca Pireddu, Simone Leo (2023):
EOSC-Life Implementation of a mechanism for publishing and sharing workflows across instances of the environment.
EOSC-Life Deliverable 2.3
https://doi.org/10.5281/zenodo.7886545

Johan Gustafsson, Georgina Samaha (2023):
Make your bioinformatics workflows findable and citable.
Make your bioinformatics workflows findable and citable, Australian BioCommons workshop, 2023-03-21.
https://doi.org/10.5281/zenodo.7787488

Ove Johan Ragnar Gustafsson (2023):
FAIR workflows.
Visible Research Software Interest Group (VRSIG), Australian Research Data Commons (ARDC), 2023-03-30.
[slides], [video] https://doi.org/10.5281/zenodo.7783773

Carole Goble (2023):
FAIR Computational Workflows.
FAIRPoints ‘Ask Me Anything’ webinar on Software & Workflows, 2023-02-21.
[video]

Romain David, Audrey S. Richard, Claire Connellan, Katharina B. Lauer, Maria Luisa Chiusano, Carole Goble, Martin Houde, Isabel Kemmer, Antje Keppler, Philippe Lieutaud, Christian Ohmann, Maria Panagiotopoulou, Sara Raza Khan, Arina Rybina, Stian Soiland-Reyes, Charlotte Wit, Rudolf Wittner, Rafael Andrade Buono, Sarah Arnaud Marsh, Pauline Audergon, Dylan Bonfils, Jose-Maria Carazo, Remi Charrel, Frederik Coppens, Wolfgang Fecke, Claudia Filippone, Eva Garcia Alvarez, Sheraz Gul, Henning Hermjakob, Katja Herzog, Petr Holub, Lukasz Kozera, Allyson L. Lister, José López-Coronado, Bénédicte Madon, Kurt Majcen, William Martin, Wolfgang Müller, Elli Papadopoulou, Christine M.A. Prat, Paolo Romano, Susanna-Assunta Sansone, Gary Saunders, Niklas Blomberg, Jonathan Ewbank (2023):
Umbrella Data Management Plans to integrate FAIR data: lessons from the ISIDORe and BY-COVID consortia for pandemic preparedness.
Data Science Journal 25
https://doi.org/10.5334/dsj-2023-035

Lucie Lamothe, Jennifer Rugaard Bregndahl Jensen, Hans Ienasescu, Johan Gustafsson, Alban Gaignard, Dmitry Repchevsky, Radka Svobodová, Tomáš Raček, Matej Antol, Magnus Palmblad, Matúš Kalaš, Hervé Ménager (2023):
An evaluation of EDAM coverage in the Tools Ecosystem and prototype integration of Galaxy and WorkflowHub systems.
BioHackrXiv
https://doi.org/10.37044/osf.io/79kje

Philip Reiner Kensche, Alexander Kanitz, Ivan Topolsky, Kim Philipp Jablonski, Pietro Mandreoli, Sven Twardziok (2023):
Executing workflows in the cloud with WESkit.
BioHackrXiv
https://doi.org/10.37044/osf.io/2z6nu

Hirotaka Suetake, Tsukasa Fukusato, Takeo Igarashi, Tazro Ohta (2023):
Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows.
GigaScience 12:giad006
https://doi.org/10.1093/gigascience/giad006

2022

Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilović, Carole Goble, and The CWL Community (2022): Methods included: standardizing computational reuse and portability with the Common Workflow Language.
Commun. ACM 65, 6 (June 2022), 54–63. https://doi.org/10.1145/3486897

Brack P, Crowther P, Soiland-Reyes S, Owen S, Lowe D, Williams AR, et al. (2022): Ten simple rules for making a software tool workflow-ready.
PLoS Comput Biol 18(3): e1009823. https://doi.org/10.1371/journal.pcbi.1009823

Beatriz Serrano-Solano, Anne Fouilloux, Ignacio Eguinoa, Matúš Kalaš, Björn Grüning, Frederik Coppens (2022):
Galaxy: A Decade of Realising CWFR Concepts.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00136

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

Stian Soiland-Reyes, Genís Bayarri, Pau Andrio, Robin Long, Douglas Lowe, Ania Niewielska, Adam Hospital, Paul Groth (2022):
Making Canonical Workflow Building Blocks interoperable across workflow languages.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00135

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

Ove Johan Ragnar Gustafsson, Tracy Chew, Georgina Samaha, Sarah Beecroft, Marco de la Pierre, Rosemarie Sadsad, Mark Gray, Gareth Price, Lisa Phippard, Nigel Ward, Andrew Lonie (2022):
Supporting the discovery and reuse of workflows in bioinformatics.
eResearch Australasia 2022, Brisbane, Australia
https://doi.org/10.5281/zenodo.7352756

Justin Clark-Casey, Carole Goble, Finn Bacall, Frederik Coppens, WorkflowHub Club (2022):
WorkflowHub: FAIR Workflow Registry.
EOSC Symposium 2022, Prague, CZ, 2022-11-14/–17
https://doi.org/10.5281/zenodo.7323471

Carole Goble, Stian Soiland-Reyes, Nick Juty (2022):
FAIR-IMPACT: T3.2.1 PIDs in data production workflows.
FAIR-IMPACT T3.2 internal meeting
https://doi.org/10.5281/zenodo.7157647

Stian Soiland-Reyes, Carole Goble (2022):
EuroScienceGateway: WP2 introduction.
European Galaxy Days, Freiburg, Germany, 2022-10-06 (Session EuroScienceGateway Kickoff)

Gareth Price, Johan Gustafsson (2022):
Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia.
Australian BioCommons Webinar
https://doi.org/10.5281/zenodo.7251310

2021

Carole Goble (2021): FAIR Computational Workflows. JOBIM 2021 (Journées Ouvertes en Biologie, Informatique et Mathématiques), 2021-07-08

Peter Wittenburg, Ivonne Anders, Christophe Blanchi, Merret Buurman, Carole Goble, Jonas Grieb, Alex Hardisty, Sharif Islam, Thomas Jejkal, Tibor Kálmán, Christine Kirkpatrick, Laurence Lannom, Thomas Lauer, Giridhar Manepalli, Karsten Peters-von Gehlen, Andreas Pfeil, Robert Quick, Mark van de Sanden, Ulrich Schwardmann, Stian Soiland-Reyes, Rainer Stotzka, Zachary Trautt, Dieter Van Uytvanck, Claus Weiland, Philipp Wieder (2022):
FAIR Digital Object Demonstrators 2021.
Report, FAIR Digital Objects Forum. Zenodo
https://doi.org/10.5281/zenodo.5872645

Raül Sirvent,
Javier Conejero, Francesc Lordan, Jorge Ejarque, Laura Rodríguez-Navas, José M. Fernández, Salvador Capella-Gutiérrez, Rosa M. Badia (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 [preprint] [slides]

Stian Soiland-Reyes (2021): RO-Crate, workflows and FAIR Digital Objects FAIR Digital Object Forum, CWFR & FDO SEM meeting, 2021-07-02 [video recording], [slides] https://doi.org/10.5281/zenodo.5060283

Laura Rodríguez-Navas (2021): WfExS: a software component to enable the use of RO-Crate in the EOSC-Life collaboratory. FAIR Digital Object Forum, CWFR & FDO SEM meeting, 2021-07-02 [video recording], [slides]

Carole Goble (2021): FAIR Computational Workflows: the what, why how and who. ICTESSH 2021 (International Conference on ICT enhanced Social Sciences and Humanities 2021), 2021-06-30

Carole Goble (2021): The EOSC-Life Workflow Collaboratory. EOSC Symposium 2021, 2021-06-17 [video recording] [slides]

Carole Goble (2021):
EOSC-Life Workflow Collaboratory.
17th IEEE e-Science Conference Infrastructures for e-Science

Laura Rodríguez-Navas (2021): WfExS: a software component to enable the use of RO-Crate in the EOSC-Life tools collaboratory. EOSC Symposium 2021, 2021-06-17 [video recording] [slides]

Stian Soiland-Reyes (2021): Capturing Just Enough Data, Software and Metadata with RO-Crate. Dataverse community meeting 2021, Software Metadata and Containerization, 2021-06-17. https://doi.org/10.5281/zenodo.4973678

Carole Goble, Stian Soiland-Reyes, Stuart Owen, Frederik Coppens (2021): Towards FAIR Workflows. _GO FAIR US webinar: FAIR Workflows, 2021-06-16 [video recording] [slides]

Carole Goble (2021): FAIR Workflows and Research Objects get a Workout. Dataverse community meeting 2021, keynote, 2021-06-15

Stian Soiland-Reyes (2021): Capturing workflow life cycle with RO-Crate. ELIXIR All Hands 2021, Workshop: Workflow Life Cycle, 2021-06-11 https://doi.org/10.5281/zenodo.4926088

Simone Leo (2021): Sustainability and Reuse: LifeMonitor. ELIXIR All Hands 2021, Workshop: Workflow Life Cycle, 2021-06-11

Stian Soiland-Reyes (2021): Data provenance with RO-Crate. EOSC-Life retreat 2021, Provenance of tools and workflows, FAIRification of workflows, 2021-05-19.

Carole Goble, Stian Soiland-Reyes (2021): RO-Crate: A framework for packaging research products into FAIR Research Objects.
RDA IG Data Fabric: FAIR Digital Objects 2021-02-25. [Video recording] [slides]

2020

Stian Soiland-Reyes, Ignacio Eguinoa (2020):
Packaging workflows with RO-Crate.
Workshop on FAIR Computational Workflows, 19th European Conference on Computational Biology (ECCB 2020).
https://doi.org/10.5281/zenodo.4011999

Simone Leo, Salvador Capella-Gutierrez (2020):
Testing workflows: Life Monitor and OpenEBench.
Workshop on FAIR Computational Workflows, 19th European Conference on Computational Biology (ECCB 2020).

Carole Goble (2020):
The WorkflowHub - a registry for workflows. The Bioschemas workflow profile.
_ 19th European Conference on Computational Biology_ (ECCB2020), virtual, 31 August 2020 – 8 September 2020.
https://doi.org/10.5281/zenodo.4012124

Posters

ELIXIR Belgium (2023):
WorkflowHub.
ELIXIR Belgium Conference 2023, Ghent, Belgium, 23-24 October 2023.
https://doi.org/10.5281/zenodo.10039763

Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodriguez-Navas, José M. Fernández, Salvador Capella-Gutierrez, Michael R. Crusoe, Björn Grüning, Smone Leo, Luca Pireddu, Marco Enrico Piras, Johan Gustafsson, Phil Ewels, WorkflowHub Community, Frederik Coppens (2023):
WorkflowHub – a fair registry for workflows.
ELIXIR All Hands 2023, Dublin, Ireland, 5-8 June 2023.
https://doi.org/10.7490/f1000research.1119430.1

Nicola Soranzo, Carole Goble (2023):
BioFAIR: a new BioCommons infrastructure for UK life science.
UKRI DRI Community Congress 2023, Birmingham, UK, 6-7 March 2023.
https://doi.org/10.5281/zenodo.7708304

Stian Soiland-Reyes, Peter Sefton, Leyla Jael Castro, Frederik Coppens, Daniel Garijo, Simone Leo, Marc Portier, Paul Groth (2022):
Creating lightweight FAIR Digital Objects with RO-Crate.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster)
Research Ideas and Outcomes 8:e93937
https://doi.org/10.3897/rio.8.e93937 [poster]

José M Fernández, Laura Rodríguez-Navas, Salvador Capella-Gutiérrez (2022):
Secured and annotated execution of workflows with WfExS-backend.
European Conference on Computational Biology (ECCB) 2022, The Global Alliance for Genomics And Health (GA4GH) 10th Plenary Meeting.
F1000Research 11:1318 (poster)
https://doi.org/10.7490/f1000research.1119198.1

Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodríguez Navas, José María Fernández, Salvador Capella-Gutierrez, Michael R. Crusoe, Björn Grüning, Simone Leo, Luca Pireddu, Johan Gustafsson, Phil Ewels, WorkflowHub Community, Frederik Coppens (2022): WorkflowHub – a FAIR registry for workflows. ELIXIR All Hands 2022, Amsterdam, Netherlands, 7-10 June 2022. https://doi.org/10.7490/f1000research.1118984.1

Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodriguez-Navas, José M. Fernández, Salvador Capella-Gutierrez, Michael R. Crusoe, Björn Grüning, Simone Leo, Luca Pireddu, Johan Gustafsson, Phil Ewels, WorkflowHub Community, Frederik Coppens (2021):
The WorkflowHub: A FAIR Registry for Workflows and Workflow Research Objects.
BOSC 2021, [poster], [abstract]

Carole Goble, Stian Soiland-Reyes, Finn Bacall, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Simone Leo, Luca Pireddu, Laura Rodríguez-Navas, José Mª Fernández, Salvador Capella-Gutierrez, Hervé Ménager, Björn Grüning, Beatriz Serrano-Solano, Philip Ewels, Frederik Coppens (2021):
Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory.
Zenodo
https://doi.org/10.5281/zenodo.4605654

Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodriguez-Navas, Kiran K Telukunta, Flora D’Anna, José M. Fernández, Alban Gaignard, Ambarish Kumar, Maciek Bak, Ivan Topolsky, Salvador Capella-Gutierrez, Michael R. Crusoe and Frederik Coppens (2020):
The Workflow Hub: A Registry of Life Science Workflows.
ISMB 2020 [video/slides], presented by Ambarish Kumar.

Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Flora D’Anna, Hervé Ménager, Laura Rodriguez-Navas, José M. Fernández, Ivan Topolsky, Alban Gaignard, Björn Grüning, Simone Leo, Luca Pireddu, Phil Ewels Maciek Bak, Salvador Capella-Gutierrez, Michael R. Crusoe and Frederik Coppens (2020):
The WorkflowHub: A FAIR Registry for Workflows and Workflow Research Objects.
International FAIR Convergence Symposium, 2020-11-27 / 2020-12-04.

WorkflowHub logo

The below logos can be used by for application, websites, posters, slides etc. for work that use, implement or support WorkflowHub and Workflow RO-Crate, linking to https://workflowhub.eu/. To ask permission for any other use, raise an issue.

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