Workflow Run RO-Crate is a working group for defining RO-Crate profiles for capturing the provenance of an execution of a computational workflow.

EuroScienceGateway will leverage a distributed computing network across 13 European countries, accessible via 6 national, user-friendly web portals, facilitating access to compute and storage infrastructures across Europe as well as to data, tools, workflows and services that can be customized to suit researchers’ needs.EuroScienceGateway will deliver a robust, scalable, seamlessly integrated open infrastructure for data-driven research, contributing an innovative and customizable service for ...

Part of T.4.1.1 Species response to environmental change (UFZ, GBIFS, UKCEH, JYU, MLU)

Part of T.4.1.2 Genetically detected biodiversity (GBIFS, UKCEH, UiO)

BioDT pipelines not associated with one of the BioDT use cases.

A general team for the EOSC4Cancer project.

This is a general team for the BGE project for any members affiliated directly or indirectly with the BGE project.

To request joining this team, make sure sure your WorkflowHub institution matches one of the listed BGE partners.

Workflows from the Industrial Biotechnology Innovation and Synthetic Biology Accelerator (IBISBA 1.0) project, which is funded by the European Union Horizon 2020 program INRAIA-02 under grant agreement 730976.

The workflows also appear on https://hub.ibisba.eu

Ongoing analysis of COVID-19 using Galaxy, BioConda and public research infrastructures https://covid19.galaxyproject.org

Team for general BY-COVID contributions

Presentations and events associated with work in FAIR Guiding Principles for Computational Workflows.

A team that gathers the workflow and workflow-related training activities related to ELIXIR, run by ELIXIR or affiliated to ELIXIR; its Hub, Nodes, platforms and communities

The ELIXIR Tools Platform helps communities find, register and benchmark software tools. These tools help researchers access, analyse and integrate biological data, and so drive scientific discovery across the life sciences.We maintain information standards for these tools, and produce, adopt and promote best practices for their development.

Part of T.4.1.3 Dynamics and threats from and for species of policy concern (UFZ, GBIFS, Naturalis, UKCEH, LifeWatchERIC)

Part of T.4.1.1 Species response to environmental change (UFZ, GBIFS, UKCEH, JYU, MLU)

Part of T.4.1.4 Species interactions with each other and with humans (GBIFS, UFZ, LifeWatchERIC, UiO)

Part of T.4.1.4 Species interactions with each other and with humans (GBIFS, UFZ, LifeWatchERIC, UiO)

Part of T.4.1.3 Dynamics and threats from and for species of policy concern (UFZ, GBIFS, Naturalis, UKCEH, LifeWatchERIC)

Part of T.4.1.2 Genetically detected biodiversity (GBIFS, UKCEH, UiO)

Background information

Task 5.2 aims to demonstrate how mobilisation of real-world population, health and care data across national borders can provide answers to policy-relevant research questions. Eventually, it aims to prototype a workflow that is standard for population health research. Here, the research question is approached by identifying a causal effect that allows to evaluate a public health intervention. As such, a methodology for approaching causal inference when conducting ...

This dataset is an RO-Crate representation of an execution of the tissue/tumor prediction workflow for digital pathology from crs4/deephealth-pipelines. It follows the Provenance Run Crate profile. The workflow has been run with cwltool, using the --provenance option to generate a CWLProv RO bundle, and then converted to an RO-Crate using runcrate. The input dataset is Mirax2-Fluorescence-2 by Yves Sucaet, from the MIRAX test data.

This is a training dataset for use in Galaxy materials science tutorials. These files can be used to demonstrate the AIRSS (Ab-Initio Random Structure Searching) method for finding muon stopping sites, using the UEP (Unperturbed Electrostatic Potential) technique for the optimisation stage of that method.

The files included are:

Si.cell: structure file containing atom locations Si.den_fmt: electron density data, generated with CASTEP Si.castep: CASTEP log file for the electron density calculation ...

Description

This is a training dataset for use in Galaxy materials science tutorials. These files can be compared to the output of simulations by MuSpinSim for dissipation of muon spins.

The files included are:

dissipation_theory.dat: theoretical values formatted as a MuSpinSim output experiment.dat: mock experimental values formatted as a MuSpinSim output

This dataset contains hourly values of 2m air temperature, snow depth and total precipitation from the ERA5-land reanalysis from 2015-01-01 to 2022-12-31.

The geographical area of interest corresponds to the Troms and Finnmark counties in Norway.

Along with 10.5281/zenodo.8142734 this is to be used as input to forecast vegetation browning in Troms and Finnmark using machine learning.

Description

This dataset contains 100m x 100m maps of cover fraction expressed in % ground cover per pixel for 10 base classes including moss & lichen for years 2015 to 2019.

The geographical area of interest corresponds to the Troms and Finnmark counties in Norway.

Along with 10.5281/zenodo.8142713 this is to be used as input to forecast vegetation browning in Troms and Finnmark using machine learning.

This RO-Crate contains a knowledge graph built from RO-Crates on WorkflowHub, enriched with metadata from additional sources. The source code used to create the knowledge graph, including the enrichments, is also included.

This version: 2025-08-29

Also published on Zenodo: https://doi.org/10.5281/zenodo.16995374

If your research project is producing workflows, they should be registered in WorkflowHub:

• To give visibility to the workflows created by the project, and by the different networks and communities within the project
• To give visibility to the workflows used by project
• To share workflows across the project, within project networks and externally
• To credit and cite the people making the workflows, and the networks to which they belong
• To track the new versions of workflows as they are ...

This is a project specific guide for the Bioiversity Genomics Europe (BGE project use of WorkflowHub.

The BioDT project is producing and maintaining workflows. We need to register those workflows in WorkflowHub:

1. To give visibility to the workflows created by the project and by the different networks and communities within the project
2. To give visibility to the workflows used by project that were created
3. To share workflows across the project, within project networks and externally
4. To credit and cite the people making the workflows and the networks to which they ...

The BY-COVID project is producing workflows. We need to register those workflows in WorkflowHub:

1. To give visibility to the workflows created by the project and by the different networks and communities within the project
2. To give visibility to the workflows used by project that were created
3. To share workflows across the project, within project networks and externally
4. To credit and cite the people making the workflows and the networks to which they belong
5. To track the versions of ...

The EuroScienceGateway project is producing and maintaining workflows. We need to register those workflows in WorkflowHub:

• To give visibility to the workflows created by the project and by the different networks and communities within the project
• To give visibility to the workflows used by project that were created
• To share workflows across the project, within project networks and externally
• To credit and cite the people making the workflows and the ...

Tutorial and specification for packaging IEEE 2791-2020 (BioCompute Objects/BCOs) as RO-Crate Research Objects.

BioCompute Object (BCO) is a standard (IEEE 2791-2020) for describing computational workflows for regularory submission, e.g. a genomics workflow as part of personalized medicine.

RO-Crate is a community-based specification for research data packaging of Research Objects with rich metadata, based on open standards and vocabularies like JSON-LD and schema.org.

BCO RO-Crate is the combination ...

This BioExcel best practice guide outlines the development process for writing a workflow using the Common Workflow Language (CWL), from creating and selecting tools like BioBB, through early experimentation, reuse and testing, to optimization and ensuring reproducibility before publication in workflow repositories.

To make your workflow FAIR (Findable, Accessible, Interoperable, Reusable), register it in WorkflowHub, a workflow registry with rich metadata capture for workflow discovery and sharing, and value-added services, for workflow testing (LifeMonitor), execution and publication.

The EuroScienceGateway, Biodiversity Genomics Europe and BioDT projects will use WorkflowHub to organise, share and publish their workflows.

This was Ask Me Anything and Bring Your Own Workflow (AMA & BYOW) specifically ...

EOSC-Life FAIR hackathon 2021 Session 3: Workflow & Tools FAIRification

BioCompute Object (BCO) is a standard (IEEE 2791-2020) for describing computational workflows for regularory submission, e.g. a genomics workflow as part of personalized medicine.

RO-Crate is a community-based specification for research data packaging of Research Objects with rich metadata, based on open standards and vocabularies like JSON-LD and schema.org.

BCO RO-Crate is the combination of these two approaches, packaging a BCO and the workflow it describes in a RO-Crate.

This webinar describes ...

Presented at the BioExcel Summer School 2021 this lecture introduces the BioExcel Building Blocks (BioBB).

See also part 2.

Presented at the BioExcel Summer School 2021 this lecture shows how to use BioExcel Building Blocks (BioBB).

See also part 1.

The results of the mentimeter for the FAIR workflows section of the EOSC-Life 3rd Open Call projects pre-hackathon induction

This BioExcel best practice guide discusses the workflow engines available for the Common Workflow Language (CWL).

In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields ...

WorkflowHub Knowledge Graph

A tool to generate a knowledge graph from a source of RO Crates. By default, this tool sources and generates an RDF graph of crates from WorkflowHub.

[![Python linting and ...

rquest-omop-worker-workflows

Source for workflow definitions for the open source RQuest OMOP Worker tool developed for Hutch/TRE-FX

Note: ARM workflows are currently broken. x86 ones work.

Inputs

### Body Sample input payload:

{ 
"task_id": "job-2023-01-13-14: 20: 38-", 
"project": "", 
"owner": "", 
"cohort": { 
"groups": [ 
{ 
"rules": [ 
{ 
"varname": "OMOP", 
"varcat": "Person", 
"type": "TEXT", 
"oper": "=", 
"value": "8507" 
} 
], 
"rules_oper": "AND" 
} 
], 
"groups_oper": "OR" 
}, 
"collection":
...

This is an experimental KNIME workflow of using the BioExcel building blocks to implement the Protein MD Setup tutorial for molecular dynamics with GROMACS.

Note that this workflow won't import in KNIME without the experimental KNIME nodes for BioBB - contact Adam Hospital for details.

This PyCOMPSs workflow tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) in PyCOMPSs for execution on HPC. Three variants of the MD Setup workflows are included, supporting a list of structures, a list of mutations, or a cumulative set of mutations.

Collection of workflows used or developed by the EuroScienceGateway project.

Workflows developed by or used by BY-COVID project.

This is a general collection of workflows used by or developed by members of the BGE project.

The Vertebrate Genomes Pipelines in Galaxy are intended to allow a user to generate high-quality near error-free assemblies of species from a user's own data or from the GenomeArk database.

Selection of BioExcel Building Blocks (BioBB) Workflows, across three workflow languages (jupyter notebooks, CWL, and Galaxy), demonstrating the use of BioBB tool descriptors for each of these systems.

Selection of BioExcel Building Blocks (BioBB) Workflows intended for tutorials and training.