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 ...

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

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 ...

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 ...

RepeatMasking Workflow

This workflow uses RepeatModeler and RepeatMasker for genome analysis.

• RepeatModeler is a software package for identifying and modeling de novo families of transposable elements (TEs). At the heart of RepeatModeler are three de novo repeat search programs (RECON, RepeatScout and LtrHarvest/Ltr_retriever) which use complementary computational methods to identify repeat element boundaries and family relationships from sequence data.

• RepeatMasker is a program that analyzes ...

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.

This workflow uses eggNOG mapper and InterProScan for functional annotation of protein sequences.

This workflow allows for genome annotation using Maker and evaluates the quality of the annotation.

This workflow runs the FEELnc tool to annotate long non-coding RNAs. Before annotating these long non-coding RNAs, StringTie will be used to assemble the RNA-seq alignments into potential trancriptions. The gffread tool provides a genome annotation file in GTF format.

This workflow analyses a given astrophysics text (e.g. Astronomer's Telegram https://astronomerstelegram.org/). It extracts positions of mentioned astronomical sources and provides possible optical counter-parts with photometric data. The corresponding photometric data can be further used to estimate the redshit of the optical sources, that is a measure of the distance between the Earth and the optical source.

Given the fact that the the tool that estimates the photometric redshift is still in ...

Automated workflow to validate Galaxy endpoint reliability using daily test runs of Falco and Bowtie2 via the SABER package. Designed for lightweight, scalable monitoring across multiple instances.

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 ...

Collection of workflows used or developed by the EuroScienceGateway project.