title: FAIR Computational Workflows
title: Workshop at the International FAIR Convergence Symposium 2020
titleType: Subtitle
Creators: name: Cohen-Boulakia, Sarah
name: Garijo, Daniel
name: Goble, Carole
name: Crusoe, Mihael R
name: Droesbeke, Bert
name: Eguinoa, Ignacio
name: Gaignard, Alban
name: Garijo, Daniel
name: Grüning, Björn
name: Lemoine, Frédéric
name: Michotey, Célia
name: Pommier, Cyril
name: Ferreira da Silva, Rafael
name: Soiland-Reyes, Stian
name: Vanschoren, Joaquin
Publisher: name: Zenodo
Year: 2020

description: Scientific workflows capture precise descriptions of the steps and data dependencies needed to carry out computational experiments in many areas of Science, ranging from Astrophysics to Bioinformatics or Geosciences. In order to promote long-term usability and uptake by the scientific community, workflows (as well as the tools that integrate them) should become findable, accessible, understandable, reusable, and 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, guidelines and best practices has been under development to reduce the time needed to adapt, reuse and extend existing scientific workflows. 
description: Session Organisers: Sarah Cohen-Boulakia, Daniel Garijo, Carole Goble 

The workshop will be divided in two parts. The first part will invite developers and users of several workflow systems, to focus a very short presentation (5-7 min) around a series of topics for making workflows FAIR.

The tour will through



The use of scientific workflow management systems including Galaxy, Snakemake, NextFlow or scripts and Notebooks to analyse data and produce FAIR data. Here, each participant will be invited to describe a given use case (a concrete workflow developed) and state how FAIR is such a workflow and/or how FAIR is the data produced by an execution of such a workflow.


Other short talks may be dedicated to short demos of tools to make workflows FAIR and include (but not limited to)



Workflow repositories that allow publication and discovery of published workflows and their execution traces (e.g., workflowhub.eu, OpenML, etc.)


The second part of the workshop will consist of a panel and community discussion (details on the schedule).

Schedule

Monday November 30th (Europe/US friendly - Afternoon Europe)

120 min

All times are WET (UK)

15:00 Introduction Sarah Cohen-Boulakia (University Paris-Saclay), Daniel Garijo (ISI, USC)

15:10 - 15:45 : Tools for FAIR workflows - Pitch talks of 5 min 

Chair : Daniel Garijo



Michael R. Crusoe (CWL; VU Amsterdam, ELIXIR-NL): The CWL Standards support the FAIR Principles

Carole Goble (ELIXIR-UK; EOSC-Life; The University of Manchester): The WorkflowHub.eu FAIR workflow registry

Stian Soiland-Reyes (BioExcel; The University of Manchester): RO-Crate for FAIR workflow packaging

Joaquin Vanschoren (OpenML community): Sharing machine learning workflows with OpenML.

Rafael Ferreira da Silva(ISI, USC): FAIR Workflow Traces for Scientific Workflow Research and Development (workflowhub.org)


15:45 - 16:45 Feedbacks from workflow users & developers - Pitch talks of 5 min

Chair : Sarah Cohen-Boulakia

Jupyter Notebooks 



Daniel Garijo (ISI, USC): From notebooks to FAIR workflows


Galaxy



Björn Grüning (Galaxy Europe, ELIXIR-DE): Complex synchronous and asynchronous workflows - from Metagenomics and COVID-19 research to Drug-Design and Climate science.

Ignacio Eguinoa (VIB): Managing provenance data from workflow execution using Galaxy and RO-Crate.

Bert Droesbeke (VIB): Galaxy workflows for COVID e.g. cleanup of viral reads and submission to ENA, containers for training workflows


Nextflow



Célia Michotey & Cyril Pommier (INRAE, ELIXIR-FR): Reproducible indexation using Nextflow for FAIDARE, a FAIR plant data discovery portal

Frédéric Lemoine (Institut Pasteur) : FAIR phylogenetic workflows with Nextflow


Snakemake



Alban Gaignard (CNRS, ELIXIR-FR): Towards more findable and reusable produced data - knowledge graphs, provenance instrumented workflows and tools registries


16:45 Discussion

Panel and community discussion. All speakers (and other participants of the session) will be invited to participate to give their opinion on a series of topics and questions raised by the organizers to help push forward a common agenda towards addressing FAIR workflows. This discussion will help inform community surveys and metadata standards for helping describing and understanding scientific workflows.

Panel - Examples of questions



Why is workflow understanding hard?

What would be appropriate metadata for workflows?

What is currently missing to make workflow reusable?

Survey/discussion on what are the most important things when looking for and browsing workflows.
description: While there are many tools for addressing different aspects of FAIR workflows, many challenges remain for describing, annotating, and exposing scientific workflows so that they can be found, understood and reused by other scientists. 

This workshop will provide a forum to discuss and review the core FAIR principles for computational workflows both considering the problem of designing and developing FAIR workflows and evaluating the ability of workflows (computational analysis pipelines) to provide FAIR data and FAIR software.

As a result, we aim to obtain feedback from the scientific workflow community of users and developers to better understand the current limitations and what are the next steps (in terms of guidelines or standardization activities) to push forward.

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.

Students aiming to learn and reuse existing methods and practices from others.