Stian Soiland-Reyes

According to our database, Stian Soiland-Reyes authored at least 54 papers between 2008 and 2024.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of three.

2024

Evaluating FAIR Digital Object and Linked Data as distributed object systems.

Stian Soiland-Reyes, Carole A. Goble, Paul Groth

PeerJ Comput. Sci., 2024

WorkflowHub: a registry for computational workflows.

Johan Gustafsson, Sean R. Wilkinson, Finn Bacall, Luca Pireddu, Stian Soiland-Reyes, Simone Leo, Stuart Owen, Nick S. Juty, José María Fernández, Björn A. Grüning, Tom Brown, Hervé Ménager, Salvador Capella-Gutiérrez, Frederik Coppens, Carole A. Goble

CoRR, 2024

Applying the FAIR Principles to Computational Workflows.

Sean R. Wilkinson, Meznah Aloqalaa, Khalid Belhajjame, Michael R. Crusoe, Bruno de Paula Kinoshita, Luiz Gadelha, Daniel Garijo, Ove Johan Ragnar Gustafsson, Nick S. 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 A. Goble

CoRR, 2024

2023

Umbrella Data Management Plans to Integrate FAIR Data: Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness.

Romain David, Audrey S. Richard, Claire Connellan, Katharina B. Lauer, Maria Luisa Chiusano, Carole A. 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, José María Carazo, Remi Charrel, Frederik Coppens, Wolfgang Fecke, Claudia Filippone, Eva G. 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

Data Sci. J., January, 2023

Recording provenance of workflow runs with 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-Gutiérrez, Renske de Wit, Bruno de Paula Kinoshita, Stian Soiland-Reyes

CoRR, 2023

The EOSC-Life Workflow Collaboratory for the Life Sciences.

Carole A. Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodríguez-Navas, José María Fernández, Björn A. Grüning, Simone Leo, Luca Pireddu, Michael R. Crusoe, Johan Gustafsson, Salvador Capella-Gutiérrez, Frederik Coppens

Proceedings of the 1st Conference on Research Data Infrastructure - Connecting Communities, 2023

RO-Crates Meets FAIR Digital Objects.

Leyla Jael Castro, Stian Soiland-Reyes, Dietrich Rebholz-Schuhmann

Proceedings of the 1st Conference on Research Data Infrastructure - Connecting Communities, 2023

2022

Ten simple rules for making a software tool workflow-ready.

Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R. Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn A. Grüning, Ignacio Eguinoa, Philip Ewels, Carole A. Goble

PLoS Comput. Biol., 2022

Making Canonical Workflow Building Blocks Interoperable across Workflow Languages.

Stian Soiland-Reyes, Genis Bayarri, Pau Andrio, Robin Long, Douglas Lowe, Ania Niewielska, Adam Hospital, Paul Groth

Data Intell., 2022

The Specimen Data Refinery: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections.

Alex R. Hardisty, Paul Brack, Carole A. Goble, Laurence Livermore, Ben Scott, Quentin Groom, Stuart Owen, Stian Soiland-Reyes

Data Intell., 2022

Packaging research artefacts with RO-Crate.

Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José María Fernández, Daniel Garijo, Björn A. Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole A. Goble

Data Sci., 2022

Methods included.

Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojsa Tijanic, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilovic, Carole A. Goble, The Cwl Community

Commun. ACM, 2022

2021

Semantic micro-contributions with decentralized nanopublication services.

Tobias Kuhn, Ruben Taelman, Vincent Emonet, Haris Antonatos, Stian Soiland-Reyes, Michel Dumontier

PeerJ Comput. Sci., 2021

Perspectives on automated composition of workflows in the life sciences.

Anna-Lena Lamprecht, Magnus Palmblad, Jon C. Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutiérrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole A. Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik D. Jagtap, Matús Kalas, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szaniszlo Szoke, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft

F1000Research, 2021

Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development.

Rafael Ferreira da Silva, Henri Casanova, Kyle Chard, Tainã Coleman, Dan Laney, Dong H. Ahn, Shantenu Jha, Dorran Howell, Stian Soiland-Reyes, Ilkay Altintas, Douglas Thain, Rosa Filgueira, Yadu N. Babuji, Rosa M. Badia, Bartosz Balis, Silvina Caíno-Lores, Scott Callaghan, Frederik Coppens, Michael R. Crusoe, Kaushik De, Frank Di Natale, Tu Mai Anh Do, Bjoern Enders, Thomas Fahringer, Anne Fouilloux, Grigori Fursin, Alban Gaignard, Alex Ganose, Daniel Garijo, Sandra Gesing, Carole A. Goble, Adil Hasan, Sebastiaan Huber, Daniel S. Katz, Ulf Leser, Douglas Lowe, Bertram Ludäscher, Ketan Maheshwari, Maciej Malawski, Rajiv Mayani, Kshitij Mehta, André Merzky, Todd S. Munson, Jonathan Ozik, Loïc Pottier, Sashko Ristov, Mehdi Roozmeh, Renan Souza, Frédéric Suter, Benjamín Tovar, Matteo Turilli, Karan Vahi, Alvaro Vidal-Torreira, Wendy R. Whitcup, Michael Wilde, Alan R. Williams, Matthew Wolf, Justin M. Wozniak

CoRR, 2021

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

Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojsa Tijanic, Hervé Ménager, Stian Soiland-Reyes, Carole A. Goble

CoRR, 2021

Workflows Community Summit: Bringing the Scientific Workflows Community Together.

Rafael Ferreira da Silva, Henri Casanova, Kyle Chard, Dan Laney, Dong H. Ahn, Shantenu Jha, Carole A. Goble, Lavanya Ramakrishnan, J. Luc Peterson, Bjoern Enders, Douglas Thain, Ilkay Altintas, Yadu N. Babuji, Rosa M. Badia, Vivien Bonazzi, Tainã Coleman, Michael R. Crusoe, Ewa Deelman, Frank Di Natale, Paolo Di Tommaso, Thomas Fahringer, Rosa Filgueira, Grigori Fursin, Alex Ganose, Björn A. Grüning, Daniel S. Katz, Olga A. Kuchar, Ana Kupresanin, Bertram Ludäscher, Ketan Maheshwari, Marta Mattoso, Kshitij Mehta, Todd S. Munson, Jonathan Ozik, Tom Peterka, Loic Pottier, Tim Randles, Stian Soiland-Reyes, Benjamín Tovar, Matteo Turilli, Thomas D. Uram, Karan Vahi, Michael Wilde, Matthew Wolf, Justin M. Wozniak

CoRR, 2021

A Community Roadmap for Scientific Workflows Research and Development.

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 A. Goble, Dorran Howell, Shantenu Jha, Daniel S. Katz, Daniel E. Laney, Ulf Leser, Maciej Malawski, Kshitij Mehta, Loïc Pottier, Jonathan Ozik, J. Luc Peterson, Lavanya Ramakrishnan, Stian Soiland-Reyes, Douglas Thain, Matthew Wolf

Proceedings of the 2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS), 2021

ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen And Data.

Rudolf Wittner, Petr Holub, Heimo Müller, Jörg Geiger, Carole A. Goble, Stian Soiland-Reyes, Luca Pireddu, Francesca Frexia, Cecilia Mascia, Elliot Fairweather, Jason R. Swedlow, Josh Moore, Caterina Strambio-De-Castillia, David Grunwald, Hiroki Nakae

Proceedings of the Provenance and Annotation of Data and Processes, 2021

2020

Unique, Persistent, Resolvable: Identifiers as the Foundation of FAIR.

Nick S. Juty, Sarala M. Wimalaratne, Stian Soiland-Reyes, John A. Kunze, Carole A. Goble, Tim Clark

Data Intell., 2020

FAIR Computational Workflows.

Carole A. Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober

Data Intell., 2020

The role of metadata in reproducible computational research.

Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Stian Soiland-Reyes, Karthik Ram, Jane Greenberg

CoRR, 2020

2019

Zenodo metadata JSON records as of 2019-09-16.

Stian Soiland-Reyes, Paul Groth

Dataset, November, 2019

RO-Crate, a lightweight approach to Research Object data packaging.

Eoghan Ó Carragáin, Carole A. Goble, Peter Sefton, Stian Soiland-Reyes

Proceedings of Workshop on Research Objects (RO2019), 2019

2018

Capturing interoperable reproducible workflows with Common Workflow Language.

Stian Soiland-Reyes, Farah Zaib Khan, Richard O. Sinnott, Andrew Lonie, Michael R. Crusoe, Carole A. Goble

Proceedings of Workshop on Research Objects (RO2018), 2018

Research Object Community Update.

Carole A. Goble, Stian Soiland-Reyes, Sean Bechhofer

Proceedings of Workshop on Research Objects (RO2018), 2018

The Archive and Package (arcp) URI Scheme.

Stian Soiland-Reyes, Marcos Cáceres

Proceedings of the 14th IEEE International Conference on e-Science, 2018

2017

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.

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 A. Goble

Nucleic Acids Res., 2017

Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis.

Steffen Möller, Stuart W. Prescott, Lars Wirzenius, Petter Reinholdtsen, Brad Chapman, Pjotr Prins, Stian Soiland-Reyes, Fabian Klötzl, Andrea Bagnacani, Matús Kalas, Andreas Tille, Michael R. Crusoe

Data Sci. Eng., 2017

2016

Drug Discovery and Big Linked Data.

Ronald Siebes, Victor de Boer, Bryn Williams-Jones, Stian Soiland-Reyes

Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 2016

Developing a Benchmark Suite for Semantic Web Data from Existing Workflows.

Antonis Troumpoukis, Angelos Charalambidis, Giannis Mouchakis, Stasinos Konstantopoulos, Ronald Siebes, Victor de Boer, Stian Soiland-Reyes, Daniela Digles

Proceedings of the Workshop on Benchmarking Linked Data (BLINK 2016) co-located with the 15th International Semantic Web Conference (ISWC), 2016

I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets.

Kyle Chard, Mike D'Arcy, Benjamin D. Heavner, Ian T. Foster, Carl Kesselman, Ravi K. Madduri, Alexis A. Rodriguez, Stian Soiland-Reyes, Carole A. Goble, Kristi Clark, Eric W. Deutsch, Ivo D. Dinov, Nathan D. Price, Arthur W. Toga

Proceedings of the 2016 IEEE International Conference on Big Data (IEEE BigData 2016), 2016

2015

Semantic-Web Access to Patent Annotations.

Anna Gaulton, Lee Harland, Mark Davies, George Papadatos, Antonis Loizou, Nathan Dedman, Daniela Digles, Stian Soiland-Reyes, Valery Tkachenko, Stefan Senger, John P. Overington, Nick Lynch

Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

2014

COMBINE archive: One File To Share Them All.

Frank T. Bergmann, Richard Adams, Stuart L. 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

CoRR, 2014

Community-driven development for computational biology at Sprints, Hackathons and Codefests.

Steffen Möller, Enis Afgan, Michael Banck, Raoul Jean Pierre Bonnal, Timothy Booth, John Chilton, Peter J. A. Cock, Markus Gumbel, Nomi L. Harris, Richard C. G. Holland, Matús Kalas, László Kaján, Eri Kibukawa, David R. Powell, Pjotr Prins, Jacqueline Quinn, Olivier Sallou, Francesco Strozzi, Torsten Seemann, Clare Sloggett, Stian Soiland-Reyes, William Spooner, Sascha Steinbiss, Andreas Tille, Anthony J. Travis, Roman Guimera, Toshiaki Katayama, Brad A. Chapman

BMC Bioinform., 2014

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

Frank T. Bergmann, Richard R. Adams, Stuart L. 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

BMC Bioinform., 2014

Structuring research methods and data with the research object model: genomics workflows as a case study.

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

J. Biomed. Semant., 2014

A suite of APIs for the management of research objects.

Raúl Palma, Piotr Holubowicz, Kevin R. Page, Stian Soiland-Reyes, Graham Klyne, Cezary Mazurek

Proceedings of the ISWC Developers Workshop 2014, 2014

Research Objects for Audio Processing: Capturing Semantics for Reproducibility.

Kevin R. Page, Raúl Palma, Piotr Holubowicz, Graham Klyne, Stian Soiland-Reyes, Daniel Garijo, Khalid Belhajjame, Rudolf Mayer

Proceedings of the AES International Conference on Semantic Audio 2014, 2014

2013

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud.

Katherine Wolstencroft, Robert Haines, Donal Fellows, Alan R. Williams, David Withers, Stuart Owen, Stian Soiland-Reyes, Ian Dunlop, Aleksandra Nenadic, Paul Fisher, Jiten Bhagat, Khalid Belhajjame, Finn Bacall, Alex R. Hardisty, Abraham Nieva de la Hidalga, Maria P. Balcazar Vargas, Shoaib Sufi, Carole A. Goble

Nucleic Acids Res., 2013

Web Annotation as a First-Class Object.

Paolo Ciccarese, Stian Soiland-Reyes, Tim Clark

IEEE Internet Comput., 2013

Taverna Mobile: Taverna workflows on Android.

Hyde Zhang, Stian Soiland-Reyes, Carole A. Goble

CoRR, 2013

PAV ontology: provenance, authoring and versioning.

Paolo Ciccarese, Stian Soiland-Reyes, Khalid Belhajjame, Alasdair J. G. Gray, Carole A. Goble, Tim Clark

J. Biomed. Semant., 2013

A workflow PROV-corpus based on taverna and wings.

Khalid Belhajjame, Jun Zhao, Daniel Garijo, Aleix Garrido, Stian Soiland-Reyes, Pinar Alper, Óscar Corcho

Proceedings of the Joint 2013 EDBT/ICDT Conferences, 2013

2012

From Workflows to Research Objects: An Architecture for Preserving the Semantics of Science.

Kevin R. Page, Raúl Palma, Piotr Holubowicz, Graham Klyne, Stian Soiland-Reyes, Don Cruickshank, Rafael González-Cabero, Esteban García-Cuesta, David De Roure, Jun Zhao, José Manuél Gómez-Pérez

Proceedings of the Second International Workshop on Linked Science 2012, 2012

RO-Manager: A Tool for Creating and Manipulating Research Objects to Support Reproducibility and Reuse in Sciences.

Jun Zhao, Graham Klyne, Piotr Holubowicz, Raúl Palma, Stian Soiland-Reyes, Kristina M. Hettne, José Enrique Ruiz, Marco Roos, Kevin R. Page, José Manuél Gómez-Pérez, David De Roure, Carole A. Goble

Proceedings of the Second International Workshop on Linked Science 2012, 2012

Workflow-Centric Research Objects: A First Class Citizen in the Scholarly Discourse.

Khalid Belhajjame, Óscar Corcho, Daniel Garijo, Jun Zhao, Paolo Missier, David R. Newman, Raúl Palma, Sean Bechhofer, Esteban García-Cuesta, José Manuél Gómez-Pérez, Graham Klyne, Kevin R. Page, Marco Roos, José Enrique Ruiz, Stian Soiland-Reyes, Lourdes Verdes-Montenegro, David De Roure, Carole A. Goble

Proceedings of the 2nd Workshop on Semantic Publishing, 2012

2011

Workflow forever: semantic web semantic models and tools for preserving and digitally publishing computational experiments.

Kristina M. Hettne, Stian Soiland-Reyes, Graham Klyne, Khalid Belhajjame, Matthew Gamble, Sean Bechhofer, Marco Roos, Óscar Corcho

Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, 2011

Fostering Scientific Workflow Preservation through Discovery of Substitute Services.

Khalid Belhajjame, Carole A. Goble, Stian Soiland-Reyes, David De Roure

Proceedings of the IEEE 7th International Conference on E-Science, 2011

2010

caGrid Workflow Toolkit: A Taverna based workflow tool for cancer Grid.

Wei Tan, Ravi K. Madduri, Aleksandra Nenadic, Stian Soiland-Reyes, Dinanath Sulakhe, Ian T. Foster, Carole A. Goble

BMC Bioinform., 2010

Taverna, Reloaded.

Paolo Missier, Stian Soiland-Reyes, Stuart Owen, Wei Tan, Aleksandra Nenadic, Ian Dunlop, Alan R. Williams, Tom Oinn, Carole A. Goble

Proceedings of the Scientific and Statistical Database Management, 2010

2009

Scientific Workflows as Services in caGrid: A Taverna and gRAVI Approach.

Wei Tan, Kyle Chard, Dinanath Sulakhe, Ravi K. Madduri, Ian T. Foster, Stian Soiland-Reyes, Carole A. Goble

Proceedings of the IEEE International Conference on Web Services, 2009

2008

Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data.

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

BMC Bioinform., 2008

Automated manipulation of systems biology models using libSBML within Taverna workflows.

Peter Li, Tom Oinn, Stian Soiland, Douglas B. Kell

Bioinform., 2008