Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory

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

doi:10.5281/zenodo.4605654

Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory

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

Information Management

Research output: Contribution to journal › Article

Abstract

EOSC-Life is developing a cloud-based workflow collaboratory to drive implementation of FAIR workflows across disciplines and RI boundaries, and foster tool- focused collaborations and reuse between communities via the sharing of data analysis workflows. The collaboratory aims to provide a framework for researchers and workflow specialists to use and reuse workflows

EOSC-Life has developed WorkflowHub as an inclusive workflow registry, agnostic to any Workflow Management System (WfMS). WorkflowHub aims to incorporate their workflows in partnership with the WfMS, to embed the registration of workflows in the community processes, e.g. based on pre-existing workflow repositories. The registry adopts common practices, e.g.use of GitHub repositories, and supports integration with the ecosystem of tool packages, assisted by registries (bio.tools, biocontainers), and services for testing and benchmarking workflows (OpenEBench, LifeMonitor).

Original language	English
Journal	Zenodo
DOIs	https://doi.org/10.5281/zenodo.4605654
Publication status	Published - 1 Mar 2021

Keywords

WorkflowHub
Computational Workflow
repository
FAIR Digital Object
FAIR

Access to Document

10.5281/zenodo.4605654Licence: CC BY

https://s11.no/2021/phd/workflow-collaboratory/Licence: CC BY

1 Active
2 Finished

eScience Lab
Goble, C. (PI), Soiland-Reyes, S. (PI), Andrabi, M. (Researcher), Stewart, A. (Affiliate), Bacall, F. (Researcher), Chadwick, E. (Researcher), Lowe, D. (Technical team), Nenadic, A. (Affiliate), Owen, S. (Researcher), Reed, P. (Researcher), Hambley, A. (Researcher), Sufi, S. A. (Supervisor), Woolland, O. (Technical team), Del-Pinto, W. (Researcher), Sparks, M. (Affiliate), Seip, O. (Affiliate), Slavin, P. (Researcher), Feizollah, A. (Researcher), Rajasekar, A. (PGR student), Suthar, S. A. R. (PGR student), Banerji, A. (Affiliate), Gray, A. (Affiliate), Jay, C. (Affiliate), Herrerias Azcue, F. (Researcher), Xu, F. (Affiliate), Juty, N. (Researcher), Hughes-Noehrer, L. (Affiliate), Yehudi, Y. (PGR student), Missier, P. (Researcher), Stevens, R. (Affiliate) & Aloqalaa, M. (PGR student)
1/01/15 → …
Project: Research
EOSC-Life: Providing an open collaborative space for digital biology in Europe
Goble, C. (PI), Bacall, F. (Technical team), Owen, S. (Researcher), Soiland-Reyes, S. (Researcher) & Williams, A. (Researcher)
1/03/19 → 31/08/23
Project: Research
BioExcel-2 Centre of Excellence for Computational Biomolecular Research
Goble, C. (PI), Soiland-Reyes, S. (Researcher), Long, R. (Researcher), Lowe, D. (Researcher), Woolland, O. (Researcher) & Capes, G. (Researcher)
1/01/19 → 30/06/22
Project: Research

3 Article
1 Conference contribution
1 Conference article

WorkflowHub: a registry for computational workflows
Gustafsson, O. J. R., Wilkinson, S. R., Bacall, F., Soiland-Reyes, S., Leo, S., Pireddu, L., Owen, S., Juty, N., Fernández, J. M., Brown, T., Ménager, H., Grüning, B., Capella-Gutierrez, S., Coppens, F. & Goble, C., 21 May 2025, In: Scientific Data. 12, 837.
Research output: Contribution to journal › Article › peer-review

Open Access
File
124 Downloads (Pure)
Enhancing RDM in Galaxy by integrating RO-Crate
De Geest, P., Coppens, F., Soiland-reyes, S., Eguinoa, I. & Leo, S., 12 Oct 2022, In: Research Ideas and Outcomes. 8, e95164.
Research output: Contribution to journal › Conference article › peer-review

Open Access
Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language
Crusoe, M. R., Abeln, S., Iosup, A., Amstutz, P., Chilton, J., Tijanić, N., Ménager, H., Soiland-Reyes, S., Gavrilović, B., Goble, C. A. & The CWL Community (Collaborator), 20 May 2022, In: Communications of the ACM. 65, 6, p. 54–63 10 p.
Research output: Contribution to journal › Article › peer-review

Open Access
File
258 Downloads (Pure)

FAIR Digital Objects Forum (FDO) (External organisation)
Soiland-Reyes, S. (Member)
11 Dec 2019 → …
Activity: Membership › Membership of network › Research

Cite this

Goble, C., Soiland-Reyes, S., Bacall, F., Owen, S., Williams, A., Eguinoa, I., Droesbeke, B., Leo, S., Pireddu, L., Rodríguez-Navas, L., Fernández, J. M., Capella-Gutierrez, S., Ménager, H., Grüning, B., Serrano-Solano, B., Ewels, P., & Coppens, F. (2021). Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory. Zenodo. https://doi.org/10.5281/zenodo.4605654

@article{0553256bf85b477cad9f69f39688cb6e,

title = "Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory",

abstract = "EOSC-Life is developing a cloud-based workflow collaboratory to drive implementation of FAIR workflows across disciplines and RI boundaries, and foster tool- focused collaborations and reuse between communities via the sharing of data analysis workflows. The collaboratory aims to provide a framework for researchers and workflow specialists to use and reuse workflows EOSC-Life has developed WorkflowHub as an inclusive workflow registry, agnostic to any Workflow Management System (WfMS). WorkflowHub aims to incorporate their workflows in partnership with the WfMS, to embed the registration of workflows in the community processes, e.g. based on pre-existing workflow repositories. The registry adopts common practices, e.g.use of GitHub repositories, and supports integration with the ecosystem of tool packages, assisted by registries (bio.tools, biocontainers), and services for testing and benchmarking workflows (OpenEBench, LifeMonitor).",

keywords = "WorkflowHub, Computational Workflow, repository, FAIR Digital Object, FAIR",

author = "Carole Goble and Stian Soiland-Reyes and Finn Bacall and Stuart Owen and Alan Williams and Ignacio Eguinoa and Bert Droesbeke and Simone Leo and Luca Pireddu and Laura Rodr{\'i}guez-Navas and Fern{\'a}ndez, \{Jos{\'e} Mª\} and Salvador Capella-Gutierrez and Herv{\'e} M{\'e}nager and Bj{\"o}rn Gr{\"u}ning and Beatriz Serrano-Solano and Philip Ewels and Frederik Coppens",

year = "2021",

month = mar,

day = "1",

doi = "10.5281/zenodo.4605654",

language = "English",

journal = "Zenodo",

publisher = "CERN",

}

TY - JOUR

T1 - Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory

AU - Goble, Carole

AU - Soiland-Reyes, Stian

AU - Bacall, Finn

AU - Owen, Stuart

AU - Williams, Alan

AU - Eguinoa, Ignacio

AU - Droesbeke, Bert

AU - Leo, Simone

AU - Pireddu, Luca

AU - Rodríguez-Navas, Laura

AU - Fernández, José Mª

AU - Capella-Gutierrez, Salvador

AU - Ménager, Hervé

AU - Grüning, Björn

AU - Serrano-Solano, Beatriz

AU - Ewels, Philip

AU - Coppens, Frederik

PY - 2021/3/1

Y1 - 2021/3/1

N2 - EOSC-Life is developing a cloud-based workflow collaboratory to drive implementation of FAIR workflows across disciplines and RI boundaries, and foster tool- focused collaborations and reuse between communities via the sharing of data analysis workflows. The collaboratory aims to provide a framework for researchers and workflow specialists to use and reuse workflows EOSC-Life has developed WorkflowHub as an inclusive workflow registry, agnostic to any Workflow Management System (WfMS). WorkflowHub aims to incorporate their workflows in partnership with the WfMS, to embed the registration of workflows in the community processes, e.g. based on pre-existing workflow repositories. The registry adopts common practices, e.g.use of GitHub repositories, and supports integration with the ecosystem of tool packages, assisted by registries (bio.tools, biocontainers), and services for testing and benchmarking workflows (OpenEBench, LifeMonitor).

AB - EOSC-Life is developing a cloud-based workflow collaboratory to drive implementation of FAIR workflows across disciplines and RI boundaries, and foster tool- focused collaborations and reuse between communities via the sharing of data analysis workflows. The collaboratory aims to provide a framework for researchers and workflow specialists to use and reuse workflows EOSC-Life has developed WorkflowHub as an inclusive workflow registry, agnostic to any Workflow Management System (WfMS). WorkflowHub aims to incorporate their workflows in partnership with the WfMS, to embed the registration of workflows in the community processes, e.g. based on pre-existing workflow repositories. The registry adopts common practices, e.g.use of GitHub repositories, and supports integration with the ecosystem of tool packages, assisted by registries (bio.tools, biocontainers), and services for testing and benchmarking workflows (OpenEBench, LifeMonitor).

KW - WorkflowHub

KW - Computational Workflow

KW - repository

KW - FAIR Digital Object

KW - FAIR

U2 - 10.5281/zenodo.4605654

DO - 10.5281/zenodo.4605654

M3 - Article

JO - Zenodo

JF - Zenodo

ER -

Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory

Abstract

Keywords

Access to Document

Fingerprint

Projects

eScience Lab

EOSC-Life: Providing an open collaborative space for digital biology in Europe

BioExcel-2 Centre of Excellence for Computational Biomolecular Research

Research output

WorkflowHub: a registry for computational workflows

Enhancing RDM in Galaxy by integrating RO-Crate

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

Activities

FAIR Digital Objects Forum (FDO) (External organisation)

Cite this