Publications by Stian Soiland-Reyes

2024

Rafael Ferreira da Silva, Deborah Bard, Kyle Chard, Shaun DeWitt, Ian T. Foster, Tom Gibbs, Carole Goble, William Godoy, Johan Gustafsson, Utz−Uwe Haus, Stephen Hudson, Shantenu Jha, Laila Los, Drew Paine, Frederic Suter, Logan Ward, Sean Wilkinson, Marcos Amaris, Yadu Babuji, Jonathan and Bader, Rajat Bhattarai, Wes Brewer, Paul Brunk, Silvina Caino−Lores, Henri Casanova, Daniela Cassol, Jared Coleman, Taina Coleman, Iacopo Colonnelli, Anderson Andrei Da Silva, Daniel de Oliveira, Pascal Elahi, Nour Elfaramawy, Wael Elwasif, Brian Etz, Thomas Fahringer, Wesley Ferreira, Rosa Filgueira, Jacob Fosso Tande, Luiz Gadelha, Andy Gallo, Daniel Garijo, Yiannis Georgiou, Philipp Gritsch, Patricia Grubel, Amal Gueroudji, Quentin Guilloteau, Carlo Hamalainen, Rolando Hong Enriquez, Lauren Huet, Kevin Hunter Kesling, Paula Iborra, Shiva Jahangiri, Jan Janssen, Joe Jordan, Sehrish Kanwal, Liliane Kunstmann, Fabian Lehmann, Ulf Leser, Chen Li, Peini Liu, Jakob Luettgau, Richard Lupat, Jose M. Fernandez, Ketan Maheshwari, Tanu Malik, Jack Marquez, Motohiko Matsuda, Doriana Medic, Somayeh Mohammadi, Alberto Mulone, John−Luke Navarro, Kin Wai Ng, Klaus Noelp, Bruno P. Kinoshita, Ryan Prout, Michael R. Crusoe, Sashko Ristov, Stefan Robila, Daniel Rosendo, Billy Rowell, Jedrzej Rybicki, Hector Sanchez, Nishant Saurabh, Sumit Kumar Saurav, Tom Scogland, Dinindu Senanayake, Woong Shin, Raul Sirvent, Tyler Skluzacek, Barry Sly−Delgado, Stian Soiland−Reyes, Abel Souza, Renan Souza, Domenico Talia, Nathan Tallent, Lauritz Thamsen, Mikhail Titov, Ben Tovar, Karan Vahi, Eric Vardar−Irrgang, Edite Vartina, Yuandou Wang, Merridee Wouters, Qi Yu, Ziad Al Bkhetan, Mahnoor Zulfiqar (2024):
Workflows Community Summit 2024: Future Trends and Challenges in Scientific Workflows.
Oak Ridge National Laboratory Technical Report ORNL/TM−2024/3573
Zenodo
https://doi.org/10.5281/zenodo.13844759

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

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

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 (2024):
Recording provenance of workflow runs with RO-Crate.
PLOS One 19(9):e0309210
https://doi.org/10.1371/journal.pone.0309210

Jonas Grieb, Claus Weiland, Alexander Wolodkin, Leyla Jael Castro, Stian Soiland-Reyes, Maya Beukes, Martin Jansen (2024):
Using Webby FDOs to Integrate AI Taxon Identification and Citizen Science.
Biodiversity Information Science and Standards 8:e134757
https://doi.org/10.3897/biss.8.134757

Stian Soiland-Reyes, Peter Sefton, Simone Leo, Leyla Jael Castro, Claus Weiland, Herbert Van de Sompel (2024):
Practical webby FDOs with RO-Crate and FAIR Signposting: Experiences and lessons learned.
International FAIR Digital Objects Implementation Summit 2024 (FDOF 2024), Berlin, Germany, 2024-03-20/–21.
Open Conference Proceedings (submitted)
https://s11.no/2024/webby-fdos/

Rudolf Wittner, Matej Gallo, Simone Leo, Cecilia Mascia, Francesca Frexia, Markus Plass, Stian Soiland-Reyes, Heimo Müller, Jörg Geiger, Petr Holub (2023):
Linking provenance and its metadata in multi-organizational environments of life sciences.
(Submitted)
https://research.manchester.ac.uk/en/publications/linking-provenance-and-its-metadata-in-multi-organizational-envir

Stian Soiland-Reyes, Peter Sefton, Simone Leo, Leyla Jael Castro, Claus Weiland, RO-Crate community (2024):
RO-Crate community update 2024.
(submitted)
https://research.manchester.ac.uk/en/publications/ro-crate-community-update-2024

Stian Soiland-Reyes, Stuart Wheater, Tom Giles, Carole Goble, Phil Quinlan (2024):
Five Safes RO-Crate: FAIR Digital Objects for Trusted Research Environments.
(submitted)
https://research.manchester.ac.uk/en/publications/five-safes-ro-crate-fair-digital-objects-for-trusted-research-env

Herbert Van de Sompel, Stian Soiland-Reyes (2024):
FAIR Signposting: Exposing the Topology of Digital Objects on the Web.
(submitted)
https://research.manchester.ac.uk/en/publications/fair-signposting-exposing-the-topology-of-digital-objects-on-the-

Peter Sefton, Stian Soiland-Reyes (2024):
Five ways RO-Crate data packages are important for repositories.
(submitted)
https://research.manchester.ac.uk/en/publications/five-ways-ro-crate-data-packages-are-important-for-repositories

José M. Fernández, Paula Iborra, Sébastien 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, Leyla Jael Castro, Rohitha Ravinder, Claus Weiland, Jonas Grieb, Alexander Rogers, Christophe Blanchi, Herbert Van de Sompel (2024):
BioHackEU23 report: Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas.
BioHackrXiv
https://doi.org/10.37044/osf.io/gmk2h

Mark D Wilkinson, Susanna-Assunta Sansone, Marjan Grootveld, Richard Dennis, David Hecker, Robert Huber, Stian Soiland-Reyes, Herbert Van de Sompel, Andreas Czerniak, Milo Thurston, Allyson L. Lister, Alban Gaignard (2024):
Report on “FAIR Signposting” and its uptake by the community.
EOSC FAIR Metrics and Data Quality Task Force
https://doi.org/10.5281/zenodo.10490289

Stian Soiland-Reyes, Carole Goble, Paul Groth (2024):
Evaluating FAIR Digital Object and Linked Data as distributed object systems.
PeerJ Computer Science 10:e1781
https://doi.org/10.7717/peerj-cs.1781
[arXiv 2306.07436] [RO-Crate]

2023

Tom Brown, Nick Juty, Stian Soiland-Reyes, Felix Shaw, Rutger Vos (2023): RO-Crates as a practical implementation of FAIR Digital Object to align biodiversity genomics work streams. (submitted) https://research.manchester.ac.uk/en/publications/ro-crates-as-a-practical-implementation-of-fair-digital-object-to

Leyla Jael Castro, Stian Soiland-Reyes, Dietrich Rebholz-Schuhmann (2023):
RO-Crates Meets FAIR Digital Objects.
1st Conference on Research Data Infrastructure (CoRDI 2023), 2023-09-12/–14, Karlsruhe, Germany.
Proceedings of the Conference on Research Data Infrastructure 1
https://doi.org/10.52825/cordi.v1i.396

Marjan Meurisse, Francisco Estupiñán-Romero, Javier González-Galindo, Natalia Martínez-Lizaga, Santiago Royo-Sierra, Simon Saldner, Lorenz Dolanski-Aghamanoukjan, Alexander Degelsegger-Marquez, Stian Soiland-Reyes, Nina Van Goethem, Enrique Bernal-Delgado, On Behalf of BeYond-COVID project contributors (2023):
Federated causal inference based on real-world observational data sources: application to a SARS-CoV-2 vaccine effectiveness assessment.
BMC Medical Research Methodology 23:248
https://doi.org/10.1186/s12874-023-02068-3

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

Rudolf Wittner, Petr Holub, Cecilia Mascia, Francesca Frexia, Heimo Müller, Markus Plass, Clare Allocca, Fay Betsou, Tony Burdett, Ibon Cancio, Adriane Chapman, Martin Chapman, Mélanie Courtot, Vasa Curcin, Johann Eder, Mark Elliot, Katrina Exter, Carole Goble, Martin Golebiewski, Bron Kisler, Andreas Kremer, Simone Leo, Sheng Lin-Gibson, Anna Marsano, Marco Mattavelli, Josh Moore, Hiroki Nakae, Isabelle Perseil, Ayat Salman, James Sluka, Stian Soiland-Reyes, Caterina Strambio-De-Castillia, Michael Sussman, Jason R. Swedlow, Kurt Zatloukal, Jörg Geiger (2023):
Toward a common standard for data and specimen provenance in life sciences.
Learning Health Systems
https://doi.org/10.1002/lrh2.10365

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 22:52
https://doi.org/10.5334/dsj-2023-035

2022

Daniel Arend, Sebastian Beier, laurent bouri, Marco Brandizi, Donald Hobern, Erwan Le Floch, Timo Mühlhaus, Cyril Pommier, Stuart Owen, Philippe Rocca-Serra, Thomas Rosnet, Stian Soiland-Reyes (2022):
BioHackEU22 Project 22: Plant data exchange and standard interoperability.
BioHackrXiv
https://doi.org/10.37044/osf.io/c724r

Stian Soiland-Reyes, Leyla Jael Castro, Daniel Garijo, Marc Portier, Carole Goble, Paul Groth (2022):
Updating Linked Data practices for FAIR Digital Object principles.
1st International Conference on FAIR Digital Objects (FDO 2022) (abstract).
Research Ideas and Outcomes 8:e94501
https://doi.org/10.3897/rio.8.e94501

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

Oliver Woolland, Paul Brack, Stian Soiland-Reyes, Ben Scott, Laurence Livermore (2022):
Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster)
Research Ideas and Outcomes 8:e94349
https://doi.org/10.3897/rio.8.e94349

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

Laurence Livermore, Paul Brack, Ben Scott, Stian Soiland-Reyes, Oliver Woolland (2022):
The Specimen Data Refinery: Using a scientific workflow approach for information extraction
Biodiversity Information Standards (TDWG 2022). Biodiversity Information Science and Standards 6:e93500
https://doi.org/10.3897/biss.6.93500

Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilović, Carole Goble, The CWL Community (2022):
Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language.
Communications of the ACM 65(6)
https://doi.org/10.1145/3486897
arXiv:2105.07028 [cs.DC] [pdf] [html]

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
arXiv:2108.06503 [cs.DL] [html] [RO-Crate]

Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Philip Ewels, Carole Goble (2022):
Ten Simple Rules for making a software tool workflow-ready.
PLOS Computational Biology 18(3):e1009823
https://doi.org/10.1371/journal.pcbi.1009823

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

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

Neil P. Chue Hong, Daniel S. Katz, Michelle Barker; Anna-Lena Lamprecht, Carlos Martinez, Fotis E. Psomopoulos, Jen Harrow, Leyla Jael Castro, Morane Gruenpeter, Paula Andrea Martinez, Tom Honeyman; Alexander Struck, Allen Lee, Axel Loewe, Ben van Werkhoven, Catherine Jones, Daniel Garijo, Esther Plomp, Francoise Genova, Hugh Shanahan, Joanna Leng, Maggie Hellström, Malin Sandström, Manodeep Sinha, Mateusz Kuzak, Patricia Herterich, Qian Zhang, Sharif Islam, Susanna-Assunta Sansone, Tom Pollard, Udayanto Dwi Atmojo; Alan Williams, Andreas Czerniak, Anna Niehues, Anne Claire Fouilloux, Bala Desinghu, Carole Goble, Céline Richard, Charles Gray, Chris Erdmann, Daniel Nüst, Daniele Tartarini, Elena Ranguelova, Hartwig Anzt, Ilian Todorov, James McNally, Javier Moldon, Jessica Burnett, Julián Garrido-Sánchez, Khalid Belhajjame, Laurents Sesink, Lorraine Hwang, Marcos Roberto Tovani-Palone, Mark D. Wilkinson, Mathieu Servillat, Matthias Liffers, Merc Fox, Nadica Miljković, Nick Lynch, Paula Martinez Lavanchy, Sandra Gesing, Sarah Stevens, Sergio Martinez Cuesta, Silvio Peroni, Stian Soiland-Reyes, Tom Bakker, Tovo Rabemanantsoa, Vanessa Sochat, Yo Yehudi, FAIR4RS WG (2022):
FAIR Principles for Research Software version 1.0 (FAIR4RS Principles v1.0).
Research Data Alliance
https://doi.org/10.15497/RDA00068

2021

Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft (2021):
Perspectives on automated composition of workflows in the life sciences
[version 1; peer review: 2 approved].
F1000Research 10:897
https://doi.org/10.12688/f1000research.54159.1

Rafael Ferreira da Silva, Henri Casanova, Kyle Chard, Ilkay Altintas, Rosa M Badia, Bartosz Balis, Tainã Coleman, Frederik Coppens, Frank Di Natale, Bjoern Enders, Thomas Fahringer, Rosa Filgueira, Grigori Fursin, Daniel Garijo, Carole Goble, Dorran Howell, Shantenu Jha, Daniel S. Katz, Daniel Laney, Ulf Leser, Maciej Malawski, Kshitij Mehta, Loïc Pottier, Jonathan Ozik, J. Luc Peterson, Lavanya Ramakrishnan, Stian Soiland-Reyes, Douglas Thain, Matthew Wolf (2021):
A Community Roadmap for Scientific Workflows Research and Development.
2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS)
https://doi.org/10.1109/WORKS54523.2021.00016
arXiv:2110.02168 [cs.DC]

Carole Goble, Stian Soiland-Reyes, Finn Bacall, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Simone Leo, Luca Pireddu, Laura Rodriguez-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

Tobias Kuhn, Vincent Emonet, Haris Antonatos, Stian Soiland-Reyes, Michel Dumontier (2021):
Semantic micro-contributions with decentralized nanopublication services.
PeerJ Computer Science 7:e387
https://doi.org/10.7717/peerj-cs.387

Neil P. Chue Hong, Daniel S. Katz, Michelle Barker; Anna-Lena Lamprecht, Carlos Martinez, Fotis E. Psomopoulos, Jen Harrow, Leyla Jael Castro, Morane Gruenpeter, Paula Andrea Martinez, Tom Honeyman; Alexander Struck, Allen Lee, Axel Loewe, Ben van Werkhoven, Catherine Jones, Daniel Garijo, Esther Plomp, Francoise Genova, Hugh Shanahan, Joanna Leng, Maggie Hellström, Malin Sandström, Manodeep Sinha, Mateusz Kuzak, Patricia Herterich, Qian Zhang, Sharif Islam, Susanna-Assunta Sansone, Tom Pollard, Udayanto Dwi Atmojo; Alan Williams, Andreas Czerniak, Anna Niehues, Anne Claire Fouilloux, Bala Desinghu, Carole Goble, Céline Richard, Charles Gray, Chris Erdmann, Daniel Nüst, Daniele Tartarini, Elena Ranguelova, Hartwig Anzt, Ilian Todorov, James McNally, Javier Moldon, Jessica Burnett, Julián Garrido-Sánchez, Khalid Belhajjame, Laurents Sesink, Lorraine Hwang, Marcos Roberto Tovani-Palone, Mark D. Wilkinson, Mathieu Servillat, Matthias Liffers, Merc Fox, Nadica Miljković, Nick Lynch, Paula Martinez Lavanchy, Sandra Gesing, Sarah Stevens, Sergio Martinez Cuesta, Silvio Peroni, Stian Soiland-Reyes, Tom Bakker, Tovo Rabemanantsoa, Vanessa Sochat, Yo Yehudi (2021):
FAIR Principles for Research Software (FAIR4RS Principles).
Research Data Alliance
https://doi.org/10.15497/RDA00065

2020

Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Stian Soiland-Reyes, Karthik Ram, Jane Greenberg (2020):
The role of metadata in reproducible computational research.
arXiv:2006.08589 (later published in Patterns, withdrew authorship due to The Cost of Knowledge pledge)

Rudolf Wittner, Petr Holub, Heimo Müller, Joerg Geiger, Carole Goble, Stian Soiland-Reyes, Luca Pireddu, Francesca Frexia, Cecilia Mascia, Elliot Fairweather, Jason R. Swedlow, Josh Moore, Caterina Strambio, David Grunwald, Hiroki Nakae (2021):
ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data In: Glavic B., Braganholo V., Koop D. (eds) Provenance and Annotation of Data and Processes (IPAW 2020/2021).
Lecture Notes in Computer Science 12839.
https://doi.org/10.1007/978-3-030-80960-7_16 [preprint & poster]

Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober (2020):
FAIR Computational Workflows.
Data Intelligence 2(1):108–121
https://doi.org/10.1162/dint_a_00033

Nick Juty, Sarala M. Wimalaratne, Stian Soiland-Reyes, John Kunze, Carole A. Goble, Tim Clark (2020):
Unique, Persistent, Resolvable: Identifiers as the foundation of FAIR.
Data Intelligence 2(1):30–39
https://doi.org/10.1162/dint_a_00025

2019

Farah Zaib Khan, Stian Soiland-Reyes, Richard O. Sinnott, Andrew Lonie, Carole Goble, Michael R. Crusoe (2019):
Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv.
GigaScience 8(11):giz095
https://doi.org/10.1093/gigascience/giz095

Pau Andrio, Adam Hospital, Javier Conejero, Luis Jordá, Marc Del Pino, Laia Codo, Stian Soiland-Reyes, Carole Goble, Daniele Lezzi, Rosa M. Badia, Modesto Orozco, Josep Ll. Gelpi (2019):
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows.
Scientific Data 6:169
https://doi.org/10.1038/s41597-019-0177-4

Eoghan Ó Carragáin, Carole Goble, Peter Sefton, Stian Soiland-Reyes (2019):
A lightweight approach to research object data packaging.
Bioinformatics Open Source Conference (BOSC 2019), Basel, Switzerland.
https://doi.org/10.5281/zenodo.3250687

Eoghan Ó Carragáin, Carole Goble, Peter Sefton, Stian Soiland-Reyes (2019):
RO-Crate: A lightweight approach to research object data packaging.
RO-15 at Workshop on Research Objects (RO 2019), IEEE eScience 2019, 2019-09-24, San Diego, CA, USA.
https://doi.org/10.5281/zenodo.3337883

2018

Gil Alterovitz, Dennis A Dean II, Carole Goble, Michael R Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Charles Hadley S King IV, Dan Taylor, KanakaDurga Addepalli, Elaine Johanson, Elaine E Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K Vora, Jeremy Goecks, Jianchao Yao, Jonas S Almeida, Konstantinos Krampis, Krista Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder (2018):
Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results.
PLOS Biology. 16(12):e3000099
https://doi.org/10.1371/journal.pbio.3000099 (bioXriv:191783)

Stian Soiland-Reyes, Marcos Cáceres (2018):
The Archive and Package (arcp) URI scheme.
2018 IEEE 14th International Conference on e-Science (e-Science).
https://doi.org/10.1109/eScience.2018.00018
[html] [pdf] [preprint server] [arXiv:1809.06935]

Stian Soiland-Reyes, Farah Zaib Khan, Richard O. Sinnott, Andrew Lonie, Michael R Crusoe, Carole Goble: Capturing interoperable reproducible workflows with Common Workflow Language.
Workshop on Research Objects (RO 2018), 29 Oct 2018, Amsterdam, Netherlands. https://doi.org/10.5281/zenodo.1312623

Carole Goble, Stian Soiland-Reyes, Sean Bechhofer:
Research Object Community Update.
At Workshop on Research Objects (RO 2018), 29 Oct 2018, Amsterdam, Netherlands.
https://doi.org/10.5281/zenodo.1313066

Stian Soiland-Reyes, Marcos Cáceres (2018):
The Archive and Package (arcp) URI scheme.
2018 IEEE 14th International Conference on e-Science (e-Science)
https://doi.org/10.1109/eScience.2018.00018
[preprint] [html] [pdf] [research object] arXiv:1809.06935

Natalie J Stanford, Finn Bacall, Fatemeh Zamanzad Ghavidel, Martin Golebiewski, Inge Jonassen, Rune Kleppe, Olga Krebs, Hadas Leonov, Stuart Owen, Kjell Petersen, Maja Rey, Stian Soiland-Reyes, Kidane Tekle, Andreas Weidemann, Alan Williams, Ulrike Wittig, Katy Wolstencroft, Anders Goksøyr, Jacky L. Snoep, Jon Olav Vik, Wolfgang Müller, Carole Goble (2018):
FAIR Bioinformatics computation and data management: FAIRDOM and the Norwegian Digital Life initiative.
NETTAB 2018 Network Tools and Applications in Biology.
[preprint]

2017

Steffen Möller, Stuart W. Prescott, Lars Wirzenius; Petter Reinholdtsen, Brad Chapman, Pjotr Prins, Stian Soiland-Reyes, Fabian Klötzl, Andrea Bagnacani, Matúš Kalaš, Andreas Tille, Michael R. Crusoe (2017): Robust cross-platform workflows: how technical and scientific communities collaborate to develop, test and share best practices for data analysis.
Data Science and Engineering 2:232 pp 232–244.
https://doi.org/10.1007/s41019-017-0050-4

Mark Robinson, Stian Soiland-Reyes, Michael R Crusoe, Carole Goble (2017):
Common Workflow Language Viewer. Bioinformatics Open Source Conference (BOSC) 2017, Prague, Czech Republic. https://doi.org/10.7490/f1000research.1114453.1 [abstract/slides] [poster]

Julie A McMurry, Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, Nathalie Conte, Mélanie Courtot, John Deck, Michel Dumontier, Donal K Fellows, Alejandra Gonzalez-Beltran, Philipp Gormanns, Jeffrey Grethe, Janna Hastings, Jean-Karim Hériché, Henning Hermjakob, Jon C Ison, Rafael C Jimenez, Simon Jupp, John Kunze, Camille Laibe, Nicolas Le Novère, James Malone, Maria Jesus Martin, Johanna R McEntyre, Chris Morris, Juha Muilu, Wolfgang Müller, Philippe Rocca-Serra, Susanna-Assunta Sansone, Murat Sariyar, Jacky L Snoep, Stian Soiland-Reyes, Natalie J Stanford, Neil Swainston, Nicole Washington, Alan R Williams, Sarala M Wimalaratne, Lilly M Winfree, Katherine Wolstencroft, Carole Goble, Cristopher J Mungall, Melissa A Haendel, Helen Parkinson (2017):
Identifiers for the 21st century: How to design, provision, and reuse identifiers to maximize utility and impact of life science data.
PLOS Biology 15(6):e2001414 https://doi.org/10.1371/journal.pbio.2001414 [pdf]

Khan FZ, Soiland-Reyes S, Lonie A, Sinnott R. (2017):
CWL+Research Object == Complete Provenance.
Poster, Bioinformatics Open Source Conference (BOSC 2017) at ISMB/ECCB, Prague, Czech Republic.
https://doi.org/10.7490/f1000research.1114781.1

Matser V, Apostolov R, Carter A, De Groot BL, Harrow I, Hospital A et al. (2017):
Building biomolecular modelling communities through BioExcel Interest Groups.
Poster, ISMB/ECCB 2017, Prague, Czech Republic. [abstract]

2016

Kyle Chard, Mike D’ Arcy, Ben Heavner, Ian Foster, Carl Kesselman, Ravi Madduri, Alexis Rodriguez, Stian Soiland-Reyes, Carole Goble, Kristi Clark, Eric W. Deutsch, Ivo Dinov, Nathan Price, Arthur Toga (2016):
I’ll Take That to Go: Big Data Bags and Minimal Identifiers for Exchange of Large, Complex Datasets.
IEEE International Conference on Big Data 2016 5 December 2016. [preprint] https://doi.org/10.1109/BigData.2016.7840618 [pdf] [zenodo]

Antonis Troumpoukis, Angelos Charalambidis, Giannis Mouchakis, Stasinos Konstantopoulos, Ronald Siebes, Victor de Boer, Stian Soiland-Reyes, Daniela Digles (2016):
Developing a Benchmark Suite for Semantic Web Data from Existing Workflows.
Proceedings of the Workshop on Benchmarking Linked Data (BLINK 2016), co-located with the 15th International Semantic Web Conference (ISWC)
In: CEUR Workshop Proceedings 1700:04
https://doi.org/10.5281/zenodo.159568
https://ceur-ws.org/Vol-1700/paper-04.pdf

Stian Soiland-Reyes, Pinar Alper, Carole Goble (2016):
Tracking workflow execution with TavernaProv.
At PROV: Three Years Later, Provenance Week 2016.
https://doi.org/10.5281/zenodo.51314 html [pdf] [rdf] [preprint] [source]

Natalie Stanford, Finn Bacall, Martin Golebiewski, Olga Krebs, Rostyk Kuzyakiv, Quyen Nguyen, Stuart Owen, Stian Soiland-Reyes, Jakub Straszewski, {van Niekerk}, Dawie, Alan Williams, Katherine Wolstencroft, Lars Malmström, Bernd Rinn, Jacky Snoep, Wolfgang Müller, Carole Goble (2016):
FAIRDOM: Reproducible Systems Biology through FAIR Asset Management.
Reproducibility, standards and SOP in bioinformatics (NETTAB), Rome, Italy 2016-10-25. [preprint] [pdf]

Katherine Wolstencroft, Olga Krebs, Jacky L. Snoep, Natalie J. Stanford, Finn Bacall, Martin Golebiewski, Rostyk Kuzyakiv, Quyen Nguyen, Stuart Owen, Stian Soiland-Reyes, Jakub Straszewski, David D. van Niekerk, Alan R. Williams, Lars Malmström, Bernd Rinn, Wolfgang Müller, Carole Goble (2016):
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.
Nucleic Acids Research 45(D1) pp D404–D407.
https://doi.org/10.1093/nar/gkw1032

Ronald Siebes, Victor de Boer, Bryn Williams-Jones, Stian Soiland-Reyes (2016):
Drug Discovery and Big Linked Data.
Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2016, Amsterdam, Netherlands. In: CEUR Workshop Proceedings 1795:29
https://ceur-ws.org/Vol-1795/paper29.pdf

2015

Peter Amstutz, Nebojša Tijanić, Stian Soiland-Reyes, John Kern, Luka Stojanovic, Tim Pierce, John Chilton, Maxim Mikheev, Samuel Lampa, Hervé Ménager, Scott Frazer, Venkat Sai Malladi, Michael R. Crusoe (2015):
Portable workflow and tool descriptions with the CWL.
Bioinformatics Open Source Conference (BOSC 2015), Dublin, Ireland, 2015-06-10/2015-06-11. [pdf]

Matthew Gamble, Norman Morrison, Stian Soiland-Reyes, Carole Goble (2015):
Research shared: www.researchobject.org.
Bioinformatics Open Source Conference (BOSC 2015), Dublin, Ireland, 2015-06-10/2015-06-11.

Stian Soiland-Reyes, Ian Dunlop, Alan R Williams, Apache Taverna team (2015):
Apache Taverna: Sustaining research software at the Apache Software Foundation.
Bioinformatics Open Source Conference (BOSC 2015), Dublin, Ireland, 2015-06-10/2015-06-11.

Anna Gaulton, Lee Harland, Mark Davies, George Papadatos, Antonis Loizou, Nathan Dedman, Daniela Digles, Stian Soiland-Reyes, Valery Tkachenk, Stefan Senger, John P Overington, Nick Lynch (2015):
Semantic-web access to patent annotations.
SWAT4LS International Conference: Semantic web applications and tools for life sciences, Riley Auditorium, Gillespie Center, Clare College, Cambridge, England, 2015-12-07/2015-12-10.
In: CEUR Workshop Proceedings 1546:59 pp. 212-213 [abstract] (archived 2021-06-17) [poster]

2014

Raúl Palma, Piotr Hołubowicz, Kevin Page, Stian Soiland-Reyes, Graham Klyne, Cezary Mazurek (2014):
A suite of APIs for the management of research objects.
ISWC-DEV 2014: Proceedings of the ISWC Developers Workshop 2014. In: CEUR Workshop Proceedings 1268:8
[pdf]

Frank T Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K Miller, David P Nickerson, Brett G Olivier, Nicolas Rodriguez, Herbert M Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère (2014):
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
BMC Bioinformatics 15(1), p. 3 https://doi.org/10.1186/s12859-014-0369-z

Steffen Möller, Enis Afgan, Michael Banck, Raoul J P Bonnal, Timothy Booth, John Chilton, Peter J A Cock, Markus Gumbel, Nomi Harris, Richard Holland, Matúš Kalaš, László Kaján, David R. Powell, Pjotr Prins, Jacqueline Quinn, Olivier Sallou, Francesco Strozzi, Torsten Seemann, Clare Sloggett, Stian Soiland-Reyes, Sascha Steinbiss, Andreas Tille, Anthony J. Travis, Roman Valls Guimera, Toshiaki Katayama, Brad A. Chapman (2014):
Community-driven development for computational biology at Sprints, Hackathons and Codefests.
BMC Bioinformatics 15(Suppl 14):S7 Supplement NETTAB 2013.
https://doi.org/10.1186/1471-2105-15-S14-S7

Kristina M. Hettne, Harish Dharuri, Jun Zhao, Katherine Wolstencroft, Khalid Belhajjame, Stian Soiland-Reyes, Eleni Mina, Mark Thompson, Don Cruickshank, Lourdes Verdes-Montenegro, Julián Garrido, David De Roure, Óscar Corcho, Graham Klyne, Reinout van Schouwen, Peter A. C. ’t Hoen, Sean Bechhofer, Carole A. Goble, Marco Roos (2014):
Structuring research methods and data with the research object model: genomics workflows as a case study.
Journal of Biomedical Semantics 5:41
https://doi.org/10.1186/2041-1480-5-41

Kevin R. Page, Raul Palma, Piotr Hołubowicz, Graham Klyne, Stian Soiland-Reyes, Daniel Garijo, Khalid Belhajjame, and Rudolf Mayer (2014):
Research Objects for Audio Processing: Capturing Semantics for Reproducibility.
53rd Audio Engineering Society International Conference on Semantic Audio, January 2014. ISBN: 978-0-937803-96-7 [proceedings] [preprint]

2013

Paolo Ciccarese, Stian Soiland-Reyes, Khalid Belhajjame, Alasdair JG Gray, Carole Goble, Tim Clark (2013):
PAV ontology: provenance, authoring and versioning.
Journal of Biomedical Semantics 4:37
https://doi.org/10.1186/2041-1480-4-37

Paolo Ciccarese, Stian Soiland-Reyes, Tim Clark (2013):
Web Annotation as a First Class Object.
IEEE Internet Computing 17(6) pp 71-75.
https://doi.org/10.1109/MIC.2013.123 [html] [preprint] arXiv:1310.6555

Hyde Zhang, Stian Soiland-Reyes, Carole Goble (2013):
Taverna Mobile: Taverna workflows on Android.
NETTAB 2013 Workshop on “Semantic, Social, and Mobile Applications for Bioinformatics and Biomedical Laboratories”, 16-18 October 2013, Lido of Venice, Italy.
EMBnet.journal 19(B)
https://doi.org/10.14806/ej.19.B.727

Katherine Wolstencroft, Robert Haines, Donal Fellows, Alan Williams, David Withers, Stuart Owen, Stian Soiland-Reyes, Ian Dunlop, Aleksandra Nenadic, Paul Fisher, Jiten Bhagat, Khalid Belhajjame, Finn Bacall, Alex Hardisty, Abraham Nieva de la Hidalga, Maria P. Balcazar Vargas, Shoaib Sufi, Carole Goble (2013):
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud.
Nucleic Acids Research 41(W1), W557-W561.
https://doi.org/10.1093/nar/gkt328

Khalid Belhajjame, Jun Zhao, Daniel Garijo, Aleix Garrido, Stian Soiland-Reyes, Pinar Alper, Oscar Corcho (2013):
A workflow PROV-corpus based on Taverna and Wings.
Proceedings of the Joint EDBT/ICDT 2013 Workshops
https://doi.org/10.1145/2457317.2457376 [pdf] [related website]

2012

Jun Zhao, Graham Klyne, Piotr Hołubowicz, Raúl Palma, Stian Soiland-Reyes, Kristina Hettne, José Enrique Ruiz, Marco Roos, Kevin Page, José Manuel Gómez-Pérez, David De Roure, Carole Goble (2012):
RO-Manager: A Tool for Creating and Manipulating Research Objects to Support Reproducibility and Reuse in Sciences.
Proceedings of the Second International Workshop on Linked Science 2012 - Tackling Big Data, 2012-10-22.
CEUR Workshop Proceedings 951:9
https://ceur-ws.org/Vol-951/paper9.pdf

Kevin Page, Raúl Palma, Piotr Hołubowicz, Graham Klyne, Stian Soiland-Reyes, Don Cruickshank, Rafael González Cabero, Esteban Garciá Cuesta, David De Roure, Jun Zhao, José Manuel Gómez-Pérez (2012):
From Workflows to Research Objects: An Architecture for Preserving the Semantics of Science.
Proceedings of the Second International Workshop on Linked Science 2012 - Tackling Big Data, 2012-10-22.
CEUR Workshop Proceedings 951:7
https://ceur-ws.org/Vol-951/paper7.pdf

Kristina Hettne, Stian Soiland-Reyes, Graham Klyne, Khalid Belhajjame, Matthew Gamble, Sean Bechhofer, Marco Roos, Oscar Corcho (2011):
Workflow forever: Semantic Web Semantic models and tools for preserving and digitally publishing computational experiments.
ACM International Conference Proceeding Series (SWAT4LS ‘11).
https://doi.org/10.1145/2166896.2166909 [preprint]

Khalid Belhajjame, Oscar Corcho, Daniel Garijo, Jun Zhao, Paolo Missier, David R. Newman, Raul Palma, Sean Bechhofer, Esteban Garcia Cuesta, Jose Manuel Gomez-Perez, Graham Klyne, Kevin Page, Marco Roos, José Enrique Ruiz, Stian Soiland-Reyes, Lourdes Verdes-Montenegro, David De Roure, Carole Goble (2012):
Workflow-centric research objects: First class citizens in scholarly discourse.
CEUR Workshop Proceedings 903:1
https://ceur-ws.org/Vol-903/paper-01.pdf

2011

Khalid Belhajjame, Carole Goble, Stian Soiland-Reyes, David De Roure (2011): Fostering scientific workflow preservation through discovery of substitute services..
2011 7th IEEE International Conference on eScience (IEEE eScience 2011) (5-8 Dec. 2011). IEEE. 2011. p. 97-104.
https://doi.org/10.1109/eScience.2011.22

Stian Soiland-Reyes, Alan R Williams, Stuart Owen, David Withers, Carole Goble (2011):
Scufl2 - because a workflow is more than its definition.
Bioinformatics Open Source Conference (BOSC) 2011, Vienna, Austria. [abstract] [poster] [slides]

2010

Wei Tan, Ravi Madduri, Alexandra Nenadic, Stian Soiland-Reyes, Dinanath Sulakhe, Ian Foster, Carole A Goble (2010):
CaGrid Workflow Toolkit: A Taverna based workflow tool for cancer grid.
BMC Bioinformatics 11:542.
https://doi.org/10.1186/1471-2105-11-542

Paolo Missier, Stian Soiland-Reyes, Stuart Owen, Wei Tan, Alexandra Nenadic, Ian Dunlop, Alan Williams, Tom Oinn, Carole Goble (2010):
Taverna, Reloaded.
Scientific and Statistical Database Management: 22nd International Conference (SSDBM 2010), Heidelberg, Germany, June 30–July 2, 2010. In Lecture Notes in Computer Science 6187.
https://doi.org/10.1007/978-3-642-13818-8_33 [preprint]

2009

Alexandra Nenadic, Stian Soiland‐Reyes, Carole Goble (2009):
Bringing caBIG services together using Taverna.
UK e‐Science All Hands (AHM) 2009 Conference, Oxford, UK, 2009. [pdf] [slides]

Wei Tan, Kyle Chard, Dinanath Sulakhe, Ravi Madduri, Ian Foster, Stian Soiland‐Reyes, Carole Goble (2009):
Scientific workflows as services in caGrid: A Taverna and gRAVI approach.
In 2009 IEEE International Conference on Web Services (ICWS 2009)
https://doi.org/10.1109/ICWS.2009.19 [preprint]

2008

Peter Li, Juan I Castrillo, Giles Velarde, Ingo Wassink, Stian Soiland-Reyes, Stuart Owen, David Withers, Tom Oinn, Matthew R Pocock, Carole A Goble, Stephen G Oliver, Douglas B Kell (2008):
Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data.
BMC Bioinformatics 7:334
https://doi.org/10.1186/1471-2105-9-334

Peter Li, Tom Oinn, Stian Soiland, Douglas B. Kell (2008):
Automated manipulation of systems biology models using libSBML within Taverna workflows.
Bioinformatics 24(2):287-289.
https://doi.org/10.1093/bioinformatics/btm578

2006

Stian Søiland (2006):
Sequence learning in a model of the basal ganglia.
MSc thesis, NTNU.
https://doi.org/11250/251073 [thesis] [slides] [code]

Other publications

Datasets

A brief list of datasets and research objects (co)-created by Stian Soiland-Reyes (work in progress)

Other documents

Reports, specifications and deliverables (co)authored by Stian Soiland-Reyes (work in progress)

Posters

Posters presented by Stian Soiland-Reyes at conferences (work in progress)

Presentations

Presentations and talks presented by Stian Soiland-Reyes at conferences and meetings (work in progress)

Software

Software (co)developed or maintained by Stian Soiland-Reyes (work in progress)