EuroScienceGateway

ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers.

The goal of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. Ultimately, it will help them gain new insights into how living ...

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 ...

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 ...

From Obis data to Biodiversity indicators

Associated Tutorial

This workflows is part of the tutorial Obis marine indicators, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Marie Jossé

Tutorial Author(s): ...

Secondary metabolite biosynthetic gene cluster (SMBGC) Annotation using Neural Networks Trained on Interpro Signatures

Associated Tutorial

This workflows is part of the tutorial Marine Omics identifying biosynthetic gene clusters, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Associated Tutorial

This workflows is part of the tutorial From NDVI data with OpenEO to time series visualisation with Holoviews, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Marie Jossé

**Tutorial ...

This workflow allows you to annotate a genome with Helixer and evaluate the quality of the annotation using BUSCO and Genome Annotation statistics. GFFRead is also used to predict protein sequences derived from this annotation, and BUSCO and OMArk are used to assess proteome quality.

Associated Tutorial

This workflows is part of the tutorial Genome annotation with Helixer, available ...

Refining Genome Annotations with Apollo

Associated Tutorial

This workflows is part of the tutorial Refining Genome Annotations with Apollo (prokaryotes), available in the GTN

Thanks to...

Tutorial Author(s): Anthony Bretaudeau, [Helena ...

Masking repeats in a genome using RepeatMasker

Associated Tutorial

This workflows is part of the tutorial Masking repeats with RepeatMasker, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Anthony ...

Structural and functional genome annotation with Funannotate

Associated Tutorial

This workflows is part of the tutorial Genome annotation with Funannotate, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

**Workflow ...

Functional annotation of protein sequences

Associated Tutorial

This workflows is part of the tutorial Functional annotation of protein sequences, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): ...

The idea of this workflow is to compare annotation with two annotation tools that differ in their approach and operation.

Associated Tutorial

This workflows is part of the tutorial Comparison of two annotation tools - Helixer and Braker3, available in the GTN

Features

• Includes [Galaxy Workflow ...

Associated Tutorial

This workflows is part of the tutorial Finding the muon stopping site with pymuon-suite in Galaxy, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Muon ...

Associated Tutorial

This workflows is part of the tutorial A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy, available in the GTN

Thanks to...

Tutorial Author(s): Anup Kumar

Tutorial Contributor(s): [Saskia ...

From Copernicus Sentinel 5P data to panoply visualization of volcanic activity impact to atmosphere

Associated Tutorial

This workflows is part of the tutorial Sentinel 5P data visualisation, available in the GTN

Thanks to...

Workflow Author(s): Marie Jossé

Tutorial Author(s): Marie Josse ...

Process argo data with the Pangeo Ecosystem and visualise them with Ocean Data View (ODV)

Associated Tutorial

This workflows is part of the tutorial Analyse Argo data, available in the GTN

Thanks to...

Workflow Author(s): Marie Jossé

Tutorial Author(s): Marie Josse ...

Compute indicators for Champs blocs

Associated Tutorial

This workflows is part of the tutorial Champs blocs indicators, available in the GTN

Thanks to...

Tutorial Author(s): Marie Josse, Yvan Le Bras ...

Associated Tutorial

This workflows is part of the tutorial Sentinel 2 biodiversity, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Marie Josse

Tutorial Author(s): [Marie ...

Subset data on the Mediterreanean see and extract and visualise the Phosphate variable

Associated Tutorial

This workflows is part of the tutorial Ocean's variables study, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a [Galaxy ...

This workflow uses Braker3 to annotate a genome.

Associated Tutorial

This workflows is part of the tutorial Genome annotation with Braker3, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a [Galaxy Workflow ...

Introduction to Deep Learning

Associated Tutorial

This workflows is part of the tutorial Introduction to deep learning, available in the GTN

Thanks to...

Tutorial Author(s): Anup Kumar, Alireza Khanteymoori ...

Galaxy workflow for the reproduction of the results published in: Panchal, Monik, Callison, June, Skukauskas, Vainius, Gianolio, Diego, Cibin, Giannantonio, York, Andrew P E, Schuster, Manfred E, Hyde, Timothy I, Collier, Paul, Catlow, C Richard A, Gibson, Emma K (2021) Operando XAFS investigation on the effect of ash deposition on three-way catalyst used in gasoline particulate filters and the effect of the manufacturing process on the catalytic activity DOI: 10.1088/1361-648x/abfe16.

This ...

Galaxy workflow for the reproduction of the results published in: R. H. Blackmore, M. E. Rivas, G. F. Tierney, K. M. H. .Mohammed, D. Decarolis, S. Hayama, F. Venturini, G. Held, R. Arrigo, M. Amboage, P. Hellier, E. W. Lynch, M. Amri, M. Casavola, T. Eralp Erden, P. Collier, P. P. Wells (2020) The electronic structure, surface properties, and in situ N2O decomposition of mechanochemically synthesised LaMnO3 DOI: 10.1039/d0cp00793e.

This workflow is published as part of the research data submitted ...

Collection of workflows used or developed by the EuroScienceGateway project.