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Making Canonical Workflow Building Blocks Interoperable across Workflow Languages

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Standard

Making Canonical Workflow Building Blocks Interoperable across Workflow Languages. / Soiland-Reyes, Stian; Bayarri, Genís; Andrio, Pau et al.
In: Data Intelligence, Vol. 4, No. 2, 01.04.2022, p. 342-357.

Research output: Contribution to Journal/MagazineJournal articlepeer-review

Harvard

Soiland-Reyes, S, Bayarri, G, Andrio, P, Long, R, Lowe, D, Niewielska, A, Hospital, A & Groth, P 2022, 'Making Canonical Workflow Building Blocks Interoperable across Workflow Languages', Data Intelligence, vol. 4, no. 2, pp. 342-357. https://doi.org/10.1162/dint_a_00135

APA

Soiland-Reyes, S., Bayarri, G., Andrio, P., Long, R., Lowe, D., Niewielska, A., Hospital, A., & Groth, P. (2022). Making Canonical Workflow Building Blocks Interoperable across Workflow Languages. Data Intelligence, 4(2), 342-357. https://doi.org/10.1162/dint_a_00135

Vancouver

Soiland-Reyes S, Bayarri G, Andrio P, Long R, Lowe D, Niewielska A et al. Making Canonical Workflow Building Blocks Interoperable across Workflow Languages. Data Intelligence. 2022 Apr 1;4(2):342-357. Epub 2022 Mar 7. doi: 10.1162/dint_a_00135

Author

Soiland-Reyes, Stian ; Bayarri, Genís ; Andrio, Pau et al. / Making Canonical Workflow Building Blocks Interoperable across Workflow Languages. In: Data Intelligence. 2022 ; Vol. 4, No. 2. pp. 342-357.

Bibtex

@article{af0a2903754f453a94d4ac3695d17da5,
title = "Making Canonical Workflow Building Blocks Interoperable across Workflow Languages",
abstract = "We introduce the concept of Canonical Workflow Building Blocks (CWBB), a methodology of describing and wrapping computational tools, in order for them to be utilised in a reproducible manner from multiple workflow languages and execution platforms. The concept is implemented and demonstrated with the BioExcel Building Blocks library (BioBB), a collection of tool wrappers in the field of computational biomolecular simulation. Interoperability across different workflow languages is showcased through a protein Molecular Dynamics setup transversal workflow, built using this library and run with 5 different Workflow Manager Systems (WfMS). We argue such practice is a necessary requirement for FAIR Computational Workflows and an element of Canonical Workflow Frameworks for Research (CWFR) in order to improve widespread adoption and reuse of computational methods across workflow language barriers.",
keywords = "Scientific workflows, Interoperable, FAIR, Computational tools, Containers, FAIR digital object (FDO), Software packaging, BioExcel Building Blocks library (BioBB), Canonical Workflow Frameworks for Research (CWFR)",
author = "Stian Soiland-Reyes and Gen{\'i}s Bayarri and Pau Andrio and Robin Long and Douglas Lowe and Ania Niewielska and Adam Hospital and Paul Groth",
year = "2022",
month = apr,
day = "1",
doi = "10.1162/dint_a_00135",
language = "English",
volume = "4",
pages = "342--357",
journal = "Data Intelligence",
issn = "2641-435X",
publisher = "MIT Press Journals",
number = "2",

}

RIS

TY - JOUR

T1 - Making Canonical Workflow Building Blocks Interoperable across Workflow Languages

AU - Soiland-Reyes, Stian

AU - Bayarri, Genís

AU - Andrio, Pau

AU - Long, Robin

AU - Lowe, Douglas

AU - Niewielska, Ania

AU - Hospital, Adam

AU - Groth, Paul

PY - 2022/4/1

Y1 - 2022/4/1

N2 - We introduce the concept of Canonical Workflow Building Blocks (CWBB), a methodology of describing and wrapping computational tools, in order for them to be utilised in a reproducible manner from multiple workflow languages and execution platforms. The concept is implemented and demonstrated with the BioExcel Building Blocks library (BioBB), a collection of tool wrappers in the field of computational biomolecular simulation. Interoperability across different workflow languages is showcased through a protein Molecular Dynamics setup transversal workflow, built using this library and run with 5 different Workflow Manager Systems (WfMS). We argue such practice is a necessary requirement for FAIR Computational Workflows and an element of Canonical Workflow Frameworks for Research (CWFR) in order to improve widespread adoption and reuse of computational methods across workflow language barriers.

AB - We introduce the concept of Canonical Workflow Building Blocks (CWBB), a methodology of describing and wrapping computational tools, in order for them to be utilised in a reproducible manner from multiple workflow languages and execution platforms. The concept is implemented and demonstrated with the BioExcel Building Blocks library (BioBB), a collection of tool wrappers in the field of computational biomolecular simulation. Interoperability across different workflow languages is showcased through a protein Molecular Dynamics setup transversal workflow, built using this library and run with 5 different Workflow Manager Systems (WfMS). We argue such practice is a necessary requirement for FAIR Computational Workflows and an element of Canonical Workflow Frameworks for Research (CWFR) in order to improve widespread adoption and reuse of computational methods across workflow language barriers.

KW - Scientific workflows

KW - Interoperable

KW - FAIR

KW - Computational tools

KW - Containers

KW - FAIR digital object (FDO)

KW - Software packaging

KW - BioExcel Building Blocks library (BioBB)

KW - Canonical Workflow Frameworks for Research (CWFR)

U2 - 10.1162/dint_a_00135

DO - 10.1162/dint_a_00135

M3 - Journal article

VL - 4

SP - 342

EP - 357

JO - Data Intelligence

JF - Data Intelligence

SN - 2641-435X

IS - 2

ER -