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ELIXIR | Workshop on FAIR Computational Workflows

Date:

Wednesday, 2nd September

Time:

13:30 to 16:30 (CEST)

Organisers

  • Ignacio Eguinoa | VIB & ELIXIR-BE, Belgium
  • Björn Grüning | University of Freiburg & ELIXIR-DE, Germany
  • Frederik Coppens | VIB & ELIXIR-BE, Belgium
  • Carole Goble | The University of Manchester & ELIXIR-UK, United Kingdom
  • Stian Soiland-Reyes| The University of Manchester & ELIXIR-UK, United Kingdom
  • Salvador Capella-Gutierrez | Barcelona Supercomputing Center & ELIXIR-ES, Spain

Invited Speakers

  • Sarah Cohen-Boulakia | Université Paris-Saclay & ELIXIR-FR, France
  • Mateusz Kuzak | NLesC & ELIXIR-NL, Netherlands
  • Carole Goble | The University of Manchester & ELIXIR-UK, United Kingdom
  • Michael Crusoe | CWL & ELIXIR-NL, Netherlands
  • Stian Soiland-Reyes | University of Manchester &  ELIXIR-UK, United Kingdom
  • Ignacio Eguinoa | VIB & ELIXIR-BE, Belgium
  • Simone Leo | CRS4, Italy
  • Salvador Capella-Gutierrez | Barcelona Supercomputing Center & ELIXIR-ES, Spain
  • Björn Grüning | University of Freiburg & ELIXIR-DE, Germany
  • Alex Peltzer | Boehringer-Ingelheim Pharma GmbH, Germany
  • Frederik Coppens | VIB & ELIXIR-BE, Belgium

Summary

Long-term use and uptake by the life-science community requires that workflows (as well as tools) are findable, accessible, exchanged and combined with others, and further that they are citable so that author’s credit is attributed fairly and accurately. 

The work on improving the FAIRness of workflows has already started and a whole ecosystem of tools and standards has been under development to ensure the production of workflow as FAIR research products. 

In this workshop we will first review the ideas of FAIR principles for computational workflows 

The second and core part of the workshop will take participants on a tour around the current ecosystem of tools, services, standards and future developments that help researchers produce FAIR digital objects in general, and workflows in particular. The tour will through:

  • Open standards to capture workflow definitions, dependencies and execution provenance: CWL and CWLProv. 
  • Specifications for metadata definition and packaging: RO-Crate and Research Objects
  • Workflow repositories that allow publication and discovery of published workflows: workflowhub.eu
  • Connection of these objects with popular WMS such as Galaxy.

Depending on the number of attendees this will section consist of either an interactive session or a live demo. 

Last section of the workshop is reserved for discussion on future plans and ideas based on participants' experiences with workflow creation, usage and publication.

Target audience

  • Researchers looking to make their workflow available in a FAIR way and/or accessing and running published workflows and workflow executions.
  • Developers of workflow management systems (WMS) that would benefit from export and import features of workflows to/from registries, using standard formats.

Schedule

Time (CEST)
Details
13:30 - 13:35 Welcome
FAIR principles for computational workflows
13:35 - 13:55 A review on the FAIR principles for computational workflows - Sarah Cohen-Boulakia
13:55 - 14:00 A word on RDA FAIR4RS - Mateusz Kuzak
Findability and Accessibility
14:00 - 14:20 The WorkflowHub - a registry for workflows and the Bioschemas workflow profile - Carole Goble
Interoperability and Reusability
14:20 - 14:40 The Common Workflow Language and CWLProv - Michael Crusoe
14:40 - 15:00 RO-Crate - Stian Soiland-Reyes & Ignacio Eguinoa
15:00 - 15:20 Testing workflows: Life Monitor and OpenEBench - Simone Leo & Salvador Capella-Gutierrez
FAIR by WfMS
15:20 - 15:35 Galaxy - Björn Grüning
15:35 - 15:50 Nextflow - Alex Peltzer
15:50 - 16:00 Best practices for workflows

Using Git for workflow versioning and other advice

16:00 - 16:30 FAIR for Workflows:  future plans and ideas based on participants' experiences with workflow creation, usage and publication - Frederik Coppens