Making Canonical Workflow Building Blocks Interoperable across Workflow Languages

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

doi:10.5281/zenodo.5727730

Making Canonical Workflow Building Blocks Interoperable across Workflow Languages

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

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	342-357
Number of pages	16
Journal	Data Intelligence
Volume	4
Issue number	2
DOIs	https://doi.org/10.5281/zenodo.5727730 https://doi.org/10.1162/dint_a_00135
Publication status	Published - 1 Apr 2022

Keywords

Computational tools
Containers
FAIR
FAIR digital object (FDO), BioExcel Building Blocks library (BioBB), Canonical Workflow Frameworks for Research (CWFR)
Interoperable
Scientific workflows
Software packaging

Access to Document

10.5281/zenodo.5727730Licence: CC BY
10.1162/dint_a_00135Licence: CC BY

https://s11.no/2022/phd/canonical-workflow-building-blocks/Licence: CC BY

Cite this

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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.",

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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",

note = "Funding Information: This work has been done as part of the BioExcel CoE (https://www.bioexcel.eu/), a project funded by the Funding Information: This work has been done as part of the BioExcel CoE (https://www.bioexcel.eu/), a project funded by the European Union contracts H2020-INFRAEDI-02-2018 823830, and H2020-EINFRA-2015-1 675728. Additional work is funded through EOSC-Life (https://www.eosc-life.eu/) contract H2020-INFRAEOSC-2018-2 824087, and ELIXIR-CONVERGE (https://elixir-europe.org/) contract H2020-INFRADEV-2019-2 871075. Publisher Copyright: {\textcopyright} 2022 Chinese Academy of Sciences.",

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doi = "10.5281/zenodo.5727730",

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AU - Soiland-Reyes, Stian

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AU - Long, Robin

AU - Lowe, Douglas

AU - Niewielska, Ania

AU - Hospital, Adam

AU - Groth, Paul

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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.

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Making Canonical Workflow Building Blocks Interoperable across Workflow Languages

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

BioExcel-2 Centre of Excellence for Computational Biomolecular Research

FAIR Research Objects and Computational Workflows – A Linked Data Approach

Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows

Cite this

Making Canonical Workflow Building Blocks Interoperable across Workflow Languages

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Projects

BioExcel-2 Centre of Excellence for Computational Biomolecular Research

Research output

FAIR Research Objects and Computational Workflows – A Linked Data Approach

Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows

Cite this