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FAIR Computational Workflows

presentation at https://researchsoft.github.io/FAIReScience/, FAIReScience 2021 online workshop virtually co-located with the 17th IEEE International Conference on eScience (eScience 2021)

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FAIR
Computational
Workflows
Professor Carole Goble
The University of Manchester UK
EU Research Infrastructures ELIXIR, IBISBA, EOSC-Life
BioExcel Centre of Excellence
Software Sustainability Institute UK
FAIRDOM Consortium
carole.goble@manchester.ac.uk
FAIReScience, IEEE eScience, 20th September 2021
Computational Workflows for Data intensive Bioscience
prepare, analyze, and share increasing volumes of complex data
CryoEM Image Analysis
Metagenomic Pipelines
Protein Ligand
Simulation
[Adam Hospital]
[Rob Finn]
[Carlos Oscar Sorzano Sanchez]
Nature 573, 149-150 (2019)
https://doi.org/10.1038/d41586-019-02619-z
Multi-step processes to
coordinate and execute multiple
codes and handle data and
processing dependencies
Typically Data flows
Benefit from FAIR data with
machine processable metadata
A precise description
A special kind of software
Workflow Management Systems FAIR bits
Abstraction: Separation of the workflow specification from its execution & tools
FAIR stratification, FAIR all the way down
FAIR Software
FAIR Data
FAIR Data FAIR Services
Image credit: BioExcel Centre of Excellence
Composition & Portability
different
components,
codes,
languages,
third parties
Workflow Management Systems FAIR bits
Composition: modularisation, FAIR parts & dependencies, propagation of FAIR properties
FAIR all the way down, versions, parts recycled, repurposed, remixed, citable credit
Workflow System Landscape
Inter-twingled, mix and matching
Scripting
environments
Interactive Electronic
Research Notebooks
Repositories Registries
Workflow
Management
Systems & execution
platforms
https://s.apache.org/existing-workflow-systems
298 Systems
General and Specialised
General Repositories
Identifiable
Community
FAIR Principles for Workflows
Hybrid Processual Digital Objects
Method “Data” Objects
Workflows as
FAIR Software
FAIR+R and FAIR++
Quality, maturity, maintainability
The principles revised
Workflows as
FAIR Digital Objects
Data-like method objects
Associated objects
The principles adapted
Workflows as
FAIR Data Instruments
FAIRification of the dataflow
The data principles supported
C. Goble, S. Cohen-Boulakia, S.
Soiland-Reyes, D. Garijo, Y. Gil, M.R.
Crusoe, K. Peters & D. Schober. FAIR
computational workflows. Data
Intelligence 2(2020), 108–121.
doi: 10.1162/dint_a_000
Workflow Objects
Software Objects
Data FAIRification
Ad

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FAIR Computational Workflows

  • 1. FAIR Computational Workflows Professor Carole Goble The University of Manchester UK EU Research Infrastructures ELIXIR, IBISBA, EOSC-Life BioExcel Centre of Excellence Software Sustainability Institute UK FAIRDOM Consortium carole.goble@manchester.ac.uk FAIReScience, IEEE eScience, 20th September 2021
  • 2. Computational Workflows for Data intensive Bioscience prepare, analyze, and share increasing volumes of complex data CryoEM Image Analysis Metagenomic Pipelines Protein Ligand Simulation [Adam Hospital] [Rob Finn] [Carlos Oscar Sorzano Sanchez] Nature 573, 149-150 (2019) https://doi.org/10.1038/d41586-019-02619-z Multi-step processes to coordinate and execute multiple codes and handle data and processing dependencies Typically Data flows Benefit from FAIR data with machine processable metadata A precise description A special kind of software
  • 3. Workflow Management Systems FAIR bits Abstraction: Separation of the workflow specification from its execution & tools FAIR stratification, FAIR all the way down FAIR Software FAIR Data FAIR Data FAIR Services
  • 4. Image credit: BioExcel Centre of Excellence Composition & Portability different components, codes, languages, third parties Workflow Management Systems FAIR bits Composition: modularisation, FAIR parts & dependencies, propagation of FAIR properties FAIR all the way down, versions, parts recycled, repurposed, remixed, citable credit
  • 5. Workflow System Landscape Inter-twingled, mix and matching Scripting environments Interactive Electronic Research Notebooks Repositories Registries Workflow Management Systems & execution platforms https://s.apache.org/existing-workflow-systems 298 Systems General and Specialised General Repositories Identifiable Community
  • 6. FAIR Principles for Workflows Hybrid Processual Digital Objects Method “Data” Objects Workflows as FAIR Software FAIR+R and FAIR++ Quality, maturity, maintainability The principles revised Workflows as FAIR Digital Objects Data-like method objects Associated objects The principles adapted Workflows as FAIR Data Instruments FAIRification of the dataflow The data principles supported C. Goble, S. Cohen-Boulakia, S. Soiland-Reyes, D. Garijo, Y. Gil, M.R. Crusoe, K. Peters & D. Schober. FAIR computational workflows. Data Intelligence 2(2020), 108–121. doi: 10.1162/dint_a_000 Workflow Objects Software Objects Data FAIRification
  • 7. Efforts: Workflow Findability and Accessibility Registries: lifecycle support for living workflows and associated objects Identifiers: DOIs, ORCID, ROR etc Licensing, credit, attribution Support versions, reuse & remix Workflow libraries Access workflows at source, Github support Auto / manual harvested metadata Registry – execution integration Execution monitoring services Onboard WfMS platforms Metadata standards framework Metadata by stealth https://workflowhub.eu Publishing Services Journals scripts Repos Containers Deploys Tools https://dockstore.org/ Registries
  • 8. Efforts: Workflow Metadata Frameworks Metadata for machines & people, for WfMS, Registries & Services Common metadata about the workflow, tools & parameters Canonical workflow description of the steps of the workflow Type the input and outputs of the steps Run Provenance / Histories / Tests RO-Crate format for packaging a workflow, its metadata and companion objects (links to containers, data etc) for exchange, archiving, reporting, citing. FAIR Digital Object Open Communities
  • 9. Efforts: Workflow Interoperability 1. Workflow spec & WfMS interoperability: describe workflows independently of WfMS. Platform independent pipeline exchange and comparison. 2. Workflow Composability: Software interoperates through APIs and metadata standards (FAIR4RS*). Workflow-ready tools. Recycle tested & validated canonical workflow blocks. https://openwdl.org/ https://www.commonwl.org Design for FAIR Data & FAIR Workflow Reuse Review Curation Certification Governance Licence combinations Access permissions Local -> Global identifiers Best Practice * FAIR4RS First Draft of FAIR4RS principles
  • 10. Efforts: Workflow Reusability and Usability FAIR+R, FAIR++, FAIR4RS Reusable – “can be understood, modified, built upon or incorporated into other software workflows” Composability + Associated Objects + Metadata Usable – “can be executed” Containers & Packaging Testing & monitoring Execution standards APIs Tool Registry Service API checker workflows test data A2. metadata are accessible, even when the workflow is no longer available Enough metadata that a workflow is read-reproducible as a method description if it no longer runs
  • 11. Effort: Workflows as functions for FAIR Data Data FAIRification of Workflows, assisted by WfMS & reporting Challenge of diverse API & AAI landscape, formats and packaging Review Curation Certification Governance Best Practice Golden Examples Canonical workflows Manage AAI, format, packaging choices Design for FAIR Data and Reuse
  • 12. FAIR Computational Workflows Hybrid Processual Digital Objects Data + Software FAIR Principles Data FAIRification methods WfMS support FAIR takes a village Community of projects, WfMS, platforms & environments, stakeholders. Long tail pattern. Collective action by a few WfMS and services nails 80:20. FAIR by stealth. Borgman, C. L., & Bourne, P. E. (2021). Why it takes a village to manage and share data. Harvard Data Science Review (under Review), arXiv:2109.01694v1.
  • 13. EOSC-Life https://www.eosc-life.eu/ RO-Crate https://www.researchobject.org/ro-crate/ WorkflowHub https://workflowhub.eu/ Galaxy Europe https://galaxyproject.eu/ Bioschemas https://bioschemas.org/ Common Workflow Language https://www.commonwl.org/ Dockstore https://dockstore.org/ WorkflowsRI https://workflowsri.org/ Acknowledgements Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael Crusoe, Kristian Peters, Daniel Schober