1. FAIR Computational Workflows
the what, why, how and who
Professor Carole Goble
The University of Manchester UK
EU Research Infrastructures: ELIXIR, IBISBA, EOSC-Life
Centre of Excellence: BioExcel
carole.goble@manchester.ac.uk
ICTeSSH 2021, 30th June 2021
https://ictessh.uns.ac.rs/

2. The Life Sciences
from compounds &
genomics to tissue banking,
from plants to marine to
humans…
https://lifescience-ri.eu/
Life Science Research
Infrastructures
clustered together

3. Life Science RIs, European Open Science Cloud
Building a data and method commons
Equivalent to SSHOC
1000s of tools
1000s of datasets
100s of data repositories
10s of registries
800+ metadata formats
Lots of data pre-
processing, processing,
post processing, analysis,
simulations…

4. Data intensive science multi-step tool-chains
to prepare, analyze, and share increasing volumes of complex data
CryoEM Image Analysis
Metagenomic Pipelines
Drug Discovery
Gravitational Wave Analysis
Climate Modelling
Ecological Niche Modelling

5. “Workflow” is an overloaded term…..
5
Instructions how to do something
Manual Protocols, SOPs, BPM
https://marketplace.sshopencloud.eu/search?categories=workflow&order=label

6. Data intensive science multi-step processing
prepare, analyze, and share increasing volumes of complex data
a tool in the toolbox
that links together tools Computational Workflows
inputs
outputs
tools, CLI,
containers,
workflows
Flexible workflow composition
mechanisms to construct & run
executable control and data flows
Access to computational infrastructure
and datasets, interoperability of the
tools, portability of the processing.
An entry point to the cloud / commons
resources.
Specification
description
Software
Execution
WfMS
Engine
Workflow

7. SARS-CoV-2 pre-processing, variant monitoring, analysis
https://covid19.galaxyproject.org
Automated monitoring of structured
data from the European COVID-19 Data
Portal
Scalable via access to a global
distributed compute network
• Improved data quality
• Uniformly analysed data for
downstream analysis & visualisation
• Submission of data to public
archives
https://elixir-europe.org/news/covid-19-variants-galaxy
Workflows and
Workflow
Management
System

8. Distributed analysis , Pulsar network
Managed online hosted Workflow as a Service Platform
Designed for direct use by end users - 32K users
Experts build workflows that others can use with their own data
Researchers build and reuse workflows that are shared
End users also use it to access and interact with a tool
Workflow and Tool histories and reporting [Björn Grüning]

9. Those workflows in the WorkflowHub Registry
Find, publish and cite workflows and
collections. Reuse, recycle, repurpose.

10. Data pipelines
Simulation & model sweeps
Data analysis,
Combining & integrating data
One-off analysis & prototyping
Pre-cooked workflows using my data, my
models, my configurations
Remixing, repurposing computational Lego
Repetition
Reproduce
Reuse, Recycle
Automated insight?
Meta-analysis?
Hypothesis generation?

11. Computational tasks
Data pipelines
Simulation & model sweeps
Data analysis,
combining & integrating data
One-off analysis & prototyping
Pre-cooked workflows using
my data, my models, my config.
Adapting remixing, repurposing
Repetition
Reproduce
Reuse, Recycle
adaptable to your
question/data
explicit, reproducible, repeatable,
reviewable transparent method
fast prototyping
shared know-how & tested recipes
scholarly publications &
supplementary materials
using other codes and best
tools, and reusing workflows
Computational resource use
Access to datasets and tools
Secure access to sensitive data
democratising processing
and computational know-how
interoperating datasets
and accessing infrastructures

12. Sharing & Publishing Tasks: Hybrid Digital Objects of Scholarship
that can be published, cited, exchanged, reviewed, validated & reused in different ways
12
Registries
Repos Containers Hosts
Running Services
Publishing Services
Journals
FAIR and Open Workflows
Publish the method – description snapshot
Publish the software – containers, hosted
deployments, open source
Living objects – dependencies and versions
Composite objects – FAIR mixable interoperable
tools: CLI, APIs & (meta)data standards
Reusable objects – quality, maintenance, portability
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

13. Workflow Management System Framings
Computational Reproducibility
Labour saving
Knowledge sharing
Democratisation of computation analysis

14. Springer Nature, September 2019
But what’s this got to do with
Social Sciences and Humanities?
Humanities are at a pivotal moment
Social Science using new data sources
Computational Social Science
Computational Archival Science
The rise of AI and Machine Learning
Implicit workflows in notebooks and tools

15. Specimen Data Refinery NH Museum Collections
workflow ensembles, rerunning with new methods
Physical Object
Digital Object Walton S, Livermore L, Bánki O, Cubey RWN, Drinkwater R, Englund M, Goble C, Groom Q, Kermorvant C,
Rey I, Santos CM, Scott B, Williams AR, Wu Z (2020) Landscape Analysis for the Specimen Data Refinery.
Research Ideas and Outcomes 6: e57602. https://doi.org/10.3897/rio.6.e57602

16. SSH examples
with thanks - Sean Bechhofer and David De Roure
Max Cycling for music
Hathitrust HTRC
Secure text mining
protecting copyright
Music genre analysis
Music Information Retrieval
Computational Analysis of Live Music Archives
Backroom computational archival science
Vocabulary indexing on
historical documents
Processing and modelling
social media data

17. It’s not like you don’t have a lot of tools….
[Daniela Duce, SAGE Publishing, Sponsors Session]
Workflows do not only work
with non-interactive tools.
Biologists have GUI-based
interactive tools too.
They do a lot of text mining.
And a lot of non-
consumptive analysis of
cohorts (called secure federated
processing of sensitive data).

18. What about manual steps?
Our data is too messy! Our creativity & intellectual know-how!
Notebooks calling workflows
Workflow as a Service platforms (like Galaxy)
The trick is automate what can and should be automated.
as a step in a workflow or
between workflows
interacting with a tool that
is a step
Humans in the Loop

19. Workflow
System
Landscape
Scripting
environments
Electronic Research Notebooks
Workflow
Management Systems
Repositories Registries
*https://s.apache.org/existing-workflow-systems
296 Systems*

20. Difference between a workflow and a script….
Separation of the workflow specification from its execution
Specification
description
Software
Execution
Precise description of a procedure
composed of multiple steps
coordinated by input/output data
relationships.
Execution of computational and
composted processes with data
consumed & produced by each step.
WfMS
Engine
Workflow
Sub
Workflows
Tools and
codes
Parameters
Inputs
Outputs
Infrastructure
Guidance
Associated
Objects
Data
Logs /
Histories /
Provenance
Services,
e.g. Test engines
+
Related workflows
Checker workflows
Contextual Entities
Metadata Graphs
Sample input
parameters, test data

21. Ad Hoc Scripting
Labour is moved from the workflow maker to the workflow system
https://xkcd.com/2054/

22. Workflow Management System Zoo
different species with different properties, from DIY to Community Platforms
Level of the Under-Ware
Domain specialisation & tools / datatypes
User target – Command line prog -> GUI
Take up of a WfMS depends on the
“plugged-in” availability of data type
specific codes, optimised processing
and everyone else using it
Light weight frameworks and engines to
fully fledged analysis platforms
Desktop -> Cloud
Interactive, automated
*https://s.apache.org/existing-workflow-systems

23. Maintaining the Zoo theme….Snake and Whales….
https://snakemake.github.io/
Workflows are rules
Graph of jobs for automatic parallelisation
Containerisation
Documentation Reports
Portable containers

24. CASAR: running (third party) codes
Composition, Abstraction, Scalability, Automation, Reporting
Manage Mess
Help Design
Handle
Heavy lifting
Report and
Reproduce
overcome incompatibilities
shield users from complexity of access
manage control and data flow
guide and validate composition
automation
dependencies and containers
changes in infrastructure
co-localising data and processing
scalable & optimised processing
test portability
security handling
error handling and alternate swapping
systematic reporting & logging of
called codes and data lineage
User-ware
Under-ware

25. Computational Workhorses
labour-saving– science labouris
The law of computational labour & cost
conservation:
“Labour and costs do not diminish, they shift to
different people at different parts of the tech stack in
different points in the research lifecycle”
Requires infrastructure.
Needs tools to be wrapped to make them components.
Need to be able to develop, run and keep up to date.
Need to find and understand them.
Need explanations to use properly and safely.

26. Shifting and sharing labour & costs ….
DIY Personal -> Community Cooperatives, something for everyone….
TOOL
DEVELOPER
WORKFLOW
USER
SYS ADMIN WORKFLOW
DEVELOPER
& CUSTODIAN
WORKFLOW
APPLICATION USER
COMPUTATIONAL
USER
Workflow System as a Platform Workflow System as a Service
Labour
Higher tech expertise
Reach
Lower Tech expertise
Preparing & maintaining
tools & workflows
Building libraries
Customising pre-cooked workflows
Embedded in applications
Guided workflow making
Managing
deployments
Interoperable, Usable & Reusable Find and Access

27. FAIR Principles for Data
tl;dr
Persistent machine-readable and
actionable metadata
Persistent identifiers
Clear licensing
Protocols for machine accessibility
Register / Index
Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3,
160018 (2016). https://doi.org/10.1038/sdata.2016.18
https://www.go-fair.org/fair-principles/
Image credit ANDS https://www.ands.org.au/working-with-data/fairdata/training

28. FAIR Principles for Workflows
Hybrid Digital Objects of Scholarship
Bioschema.org type
Method Objects
The FAIR Data principles
can be adapted.
Software Objects
The FAIR principles
can be revised.
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 * FAIR4RS First Draft of FAIR4RS principles
Design for FAIR Data
Design for Reuse
RDA/ReSA/Force11
FAIR4Research Software WG

29. FAIR: Metadata for Machines & Access
Community efforts to describe workflows and get platforms on board to be
FAIR at source. Lots of JSON-LD
Common metadata for registration
and discovery, controlled vocabulary
Canonical workflow descriptions
machine and human readable
Type the input and outputs of the steps,
controlled vocabulary
Run Provenance
ontology
Format for run and test Records
FAIR Digital Objects
Package a workflow, its components and
associated objects, with associated
metadata into a citable object.
Format for Reporting, Exchanging
between services and Archiving.
Carrier of metadata.
Tools Registry Service API

30. Design for FAIR Data
Tools/Codes/Datasets
• enable programmatic access to data & metadata
• avoid usage restrictions on data
Workflows
• use and make FAIR identifiers for data
• license data outputs
• avoid proprietary formats
• validate parameters avoid faulty/unsafe results
• track data provenance
Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3,
160018 (2016). https://doi.org/10.1038/sdata.2016.18
The Data Principles were
primarily intended as
guidelines for machine
processable data and
metadata for automation!

31. Design for FAIR Data and Reuse – Community efforts
Quality Assured, Interoperable and Reusable Workflows and Workflow Blocks
Build libraries, Design using blocks, Workflow best practices, Register them!
IWC - Intergalactic Workflow Commission
Review and curate
Canonical descriptions
Recycle descriptions and sub-workflows
Platform independent pipeline exchange and comparison
Register and Publish

32. Workflow Services: The EOSC-Life Collaboratory
Takes a Village – people -> workflows, services and standards

33. The “Social Science” of
the Workflow Village
Open Communities working together
Regardless of organisational, project and national
boundaries. And everyone gets credit!
Dedicated Core teams.
Open Science and Open Source Software cultural
norms
Open ecosystem – no one system, no one stack.
Respect and on-board pre-existing platforms &
communities
Community clustering around systems for
economies of scale, support and sustainability

34. Workflow Registry
…
Respect the ecosystem
Credit workflow developers
and custodians
Citation & Credit
Discussion forums for
workflow developers and
users
Licensing
Analytics for impact profile
building
Rapidly released for COVID workflows
Listed in the EU COVID Data Portal
1/3rd workflows COVID related

35. Spaces, Teams, People
Linking up providers and users
Building visibility & reputation
Reciprocity to close the
“Find – Get– Use – Credit” loop
Build Knowledge Graphs linking out to
OpenAIRE, DataCite and other tools
Workflow Registry
Rapidly released for COVID workflows
Listed in the EU COVID Data Portal
1/3rd workflows COVID related

36. The magic diamond to get everyone on board
COVID provided it all
Community(ies) with leadership
for services, standards, tools, needs
Sponsorship
by projects
Championing
by systems, users, policy makers
Drivers
Users
Baked in
Purpose
Resources
Delivery
Adoption
Workflow Registry
Rapidly released for COVID workflows
Listed in the EU COVID Data Portal
1/3rd workflows COVID related

37. Lockdown has been amazingly productive and really GOOD
for this kind of pan-project, pan–organisation work
Equitable Participation

38. https://galaxyproject.org/gcc/
Community lead Capacity Building
Helping people get on board….

39. TL;DL Summary
Computational Workflows are a significant tool in the toolbox of
computational research, supporting CASAR
Research(er) productivity, democratising infrastructure, reproducibility
Labour & cost shifts – a community can get organised
Workflows are hybrid Digital Objects of scholarship – method and
software, which affects their FAIRness criteria
FAIR, workflows and their infrastructure takes a village, as does all
computational research

40. Acknowledgements
The WorkflowHub Club, Bioschemas Community, RO-Crate
Community, CWL Community, Galaxy Europe, EOSC-Life
and ELIXIR Tools Platform.
Special Thanks
Stian Soiland-Reyes (U Manchester / U Amsterdam)
David De Roure (U Oxford)
Sean Bechhofer (U Manchester)
Björn Grüning (U Freiburg)
Frederik Coppens (VIB)
EOSC-Life https://www.eosc-life.eu/
ELIXIR http://elixir-europe.org
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/

41. Extras