Publications by Stian Soiland-Reyes

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: awaiting peer review]**.
F1000Research 10:897
https://doi.org/10.12688/f1000research.54159.1

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 (2021):
Packaging research artefacts with RO-Crate.
Data Science (accepted).
arXiv:2108.06503v1 [cs.DL] [html] [RO-Crate]
https://doi.org/10.5281/zenodo.5146228

Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Carole Goble, CWL Community (2021):
Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language.
Communications of the ACM (accepted).
To appear as https://doi.org/10.1145/3486897
preprint: arXiv:2105.07028 [cs.DC]

Stian Soiland-Reyes, Genís Bayarri, Pau Andrio, Robin Long, Douglas Lowe, Ania Niewielska, Adam Hospital (2021):
Making Canonical Workflow Building Blocks interoperable across workflow languages.
Extended abstract (submitted), Zenodo https://doi.org/10.5281/zenodo.4602855

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.
Extended abstract (submitted), 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

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 [pdf]

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

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

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

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

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]

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

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]

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) CEUR Workshop Proceedings 1700(04) [pdf] [zenodo] https://doi.org/10.5281/zenodo.159568 [preprint]

Peter Amstutz, Michael R. Crusoe, Nebojša Tijanić (editors), Brad Chapman, John Chilton, Michael Heuer, Andrey Kartashov, Dan Leehr, Hervé Ménager, Maya Nedeljkovich, Matt Scales, Stian Soiland-Reyes, Luka Stojanovic (2016):
Common Workflow Language, v1.0
Specification, Common Workflow Language working group. https://w3id.org/cwl/v1.0/ https://doi.org/10.6084/m9.figshare.3115156.v2

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 [pdf] [html]

Raul 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, CEUR-WS.org online http://ceur-ws.org/Vol-1268/paper8.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

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 4:1, 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.
EMBnet.journal 19(B). At NETTAB 2013 Workshop on “Semantic, Social, and Mobile Applications for Bioinformatics and Biomedical Laboratories” 16-18 October 2013, Lido of Venice, Italy https://doi.org/10.14806/ej.19.B.727 [pdf]

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, ACM, New York, NY, USA, pp. 331–332. https://doi.org/10.1145/2457317.2457376 [pdf] [related website]

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] [escholar]