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 organisms work.
TeSS is an example of an ELIXIR resource. TeSS is online training portal that gathers life science training materials and training courses from across Europe, and allows you to search it in one website. This makes it easier for scientists to find the training they need, and gives the training courses wider publicity.
ELIXIR includes 22 members and one Observer, bringing together over 220 research organisations. It was founded in December 2013 and began implementing its first scientific programme in 2014. It is currently implementing its second five-year scientific programme.
Web page: https://elixir-europe.org/
Funding details:Related items
- People (28)
- Teams (6)
- Organizations (18)
- Data files (6)
- SOPs (3)
- Publications (26)
- Presentations (9)
- Events (8)
- Documents (1)
- Workflows (51+1)
- Collections (2)
Teams: ELIXIR Training, ELIXIR Tools platform
Organizations: VIB, ELIXIR Belgium

Teams: BioBB Building Blocks, EuroScienceGateway
Organizations: Barcelona Supercomputing Center
Teams: EuroScienceGateway
Organizations: Science and Technology Facilities Council

Teams: IBISBA Workflows, nf-core viralrecon, Testing, Defragmentation TS, EuroScienceGateway, ELIXIR Training
Organizations: The University of Manchester
Teams: GalaxyProject SARS-CoV-2, usegalaxy.be workflows, EuroScienceGateway
Organizations: ELIXIR Belgium, VIB

Teams: Australian BioCommons, Galaxy Australia, ELIXIR Training, ELIXIR Tools platform, National Computational Infrastructure (NCI) WorkflowHub team
Organizations: University of Melbourne, Australian BioCommons

Expertise: Biochemistry, Proteomics, Mass Spectrometry Imaging
Tools: Mass spectrometry, Proteomics
Teams: EuroScienceGateway
Organizations: The University of Manchester

Teams: RECETOX SpecDatRI, RECETOX, usegalaxy-eu, ELIXIR Metabolomics, Intergalactic Workflow Commission (IWC)
Organizations: Masaryk University, RECETOX

Expertise: Bioinformatics, Cheminformatics, Metabolomics, Python, R, Software Engineering, Workflows
Tools: Metabolomics, Python, R, Workflows, Mass spectrometry, Chromatography
Teams: ODA, EuroScienceGateway
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 ...
Space: ELIXIR
Public web page: https://eurosciencegateway.eu/
Start date: 1st Oct 2022
End date: 31st Aug 2025
Organisms: Not specified
Space: ELIXIR
Public web page: https://elixir-europe.org/communities/metabolomics
Organisms: Not specified
Team for general BY-COVID contributions
Space: ELIXIR
Public web page: Not specified
Organisms: Not specified
Presentations and events associated with work in FAIR Guiding Principles for Computational Workflows.
Space: ELIXIR
Public web page: https://workflows.community/groups/fair/
Organisms: Not specified
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
Space: ELIXIR
Public web page: https://elixir-europe.org
Organisms: Not specified
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.
Space: ELIXIR
Public web page: https://elixir-europe.org/platforms/tools
Organisms: Not specified
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 ...
Creators: Eli Chadwick, Muon Spectroscopy Computational Project
Submitter: Stian Soiland-Reyes
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
Creators: Patrick Austin, Muon Spectroscopy Computational Project
Submitter: Stian Soiland-Reyes
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.
Creator: Jean Iaquinta
Submitter: Stian Soiland-Reyes
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.
Creators: Jean Iaquinta, Anne Fouilloux
Submitter: Stian Soiland-Reyes
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
Creators: Eli Chadwick, Oliver Woolland, Alexander Hambley, Stian Soiland-Reyes, Volodymyr Savchenko
Submitter: Eli Chadwick
canonical record: https://zenodo.org/records/10405036
Source data (GSE182152) was analysed with WFHub:688 to generate these datasets
Creators: Helena Rasche, Iacopo Cristoferi, Marek Ostaszewski, Andrew Stubbs
Submitter: Helena Rasche
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 ...
Creators: Stian Soiland-Reyes, Carole Goble, Finn Bacall, Johan Gustafsson, Rafael Andrade Buono
Submitter: Stian Soiland-Reyes
The BY-COVID project is producing 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 networks to which they belong
- To track the versions of ...
Creators: Carole Goble, Finn Bacall, Stian Soiland-Reyes, Andrew Stubbs, Helena Rasche
Submitter: Stian Soiland-Reyes
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 ...
Creators: Stian Soiland-Reyes, Carole Goble, Finn Bacall
Submitter: Stian Soiland-Reyes
Abstract (Expand)
Authors: Frédéric Suter, Tainã Coleman, İlkay Altintaş, Rosa M. Badia, Bartosz Balis, Kyle Chard, Iacopo Colonnelli, Ewa Deelman, Paolo Di Tommaso, Thomas Fahringer, Carole Goble, Shantenu Jha, Daniel S. Katz, Johannes Köster, Ulf Leser, Kshitij Mehta, Hilary Oliver, J.-Luc Peterson, Giovanni Pizzi, Loïc Pottier, Raül Sirvent, Eric Suchyta, Douglas Thain, Sean R. Wilkinson, Justin M. Wozniak, Rafael Ferreira da Silva
Date Published: 2026
Publication Type: Journal
DOI: 10.1016/j.future.2025.107974
Citation: Future Generation Computer Systems 174:107974
Abstract (Expand)
Authors: Ove Johan Ragnar Gustafsson, Sean R. Wilkinson, Finn Bacall, Stian Soiland-Reyes, Simone Leo, Luca Pireddu, Stuart Owen, Nick Juty, José M. Fernández, Tom Brown, Hervé Ménager, Björn Grüning, Salvador Capella-Gutierrez, Frederik Coppens, Carole Goble
Date Published: 1st Dec 2025
Publication Type: Journal
DOI: 10.1038/s41597-025-04786-3
Citation: Sci Data 12(1),837
Abstract
Authors: Sean R. Wilkinson, Meznah Aloqalaa, Khalid Belhajjame, Michael R. Crusoe, Bruno de Paula Kinoshita, Luiz Gadelha, Daniel Garijo, Ove Johan Ragnar Gustafsson, Nick Juty, Sehrish Kanwal, Farah Zaib Khan, Johannes Köster, Karsten Peters-von Gehlen, Line Pouchard, Randy K. Rannow, Stian Soiland-Reyes, Nicola Soranzo, Shoaib Sufi, Ziheng Sun, Baiba Vilne, Merridee A. Wouters, Denis Yuen, Carole Goble
Date Published: 1st Dec 2025
Publication Type: Journal
DOI: 10.1038/s41597-025-04451-9
Citation: Sci Data 12(1),328
Abstract (Expand)
Authors: Armin Dadras, Oana Kaiser, Björn Grüning, Sebastian Luna-Valero, Enol Fernandez-del-Castillo
Date Published: 20th Aug 2025
Publication Type: Tech report
Citation: https://doi.org/10.5281/zenodo.16909970
Abstract (Expand)
Authors: Armin Dadras, Denys Savchenko, Andrii Neronov, Volodymyr Savchenko, Nikolay Vazov, Jean Iaquinta, Eva Alloza, María Chavero Díez, Anthony Bretaudeau
Date Published: 18th Aug 2025
Publication Type: Tech report
Citation: https://doi.org/10.5281/zenodo.16683440
Abstract (Expand)
Authors: Marco Antonio Tangaro, Stefano Nicotri, Björn Grüning, Sanjay Kumar Srikakulam, Armin Dadras, Oana Kaiser, Mira Kuntz, Anthony Bretaudeau, Paul De Geest, Sebastian Luna-Valero, María Chavero Díez, José María Fernández González, Salvador Capella-Gutierrez, Josep Lluís Gelpí, Jan Astalos, Boris Jurič, Miroslav Ruda, Łukasz Opioła, Hakan Bayındır, SILVIA GIOIOSA, Gaetanomaria De Sanctis, Federico Zambelli
Date Published: 7th Aug 2025
Publication Type: Unpublished
Citation: https://doi.org/10.5281/zenodo.16761933
Abstract (Expand)
Authors: Eli Chadwick, Oliver Woolland, Volodymyr Savchenko, Finn Bacall, Alexander Hambley, José María Fernández González, Armin Dadras, Stian Soiland-Reyes
Date Published: 1st Aug 2025
Publication Type: Tech report
Citation:
Abstract (Expand)
Authors: Armin Dadras, Marco Antonio Tangaro
Date Published: 1st Aug 2025
Publication Type: Tech report
Citation: https://doi.org/10.5281/zenodo.16764158
Abstract (Expand)
Author: Smitesh Jain
Date Published: 17th Jul 2025
Publication Type: Tech report
Citation: https://doi.org/10.5281/zenodo.16030329
Abstract (Expand)
Authors: Sean R. Wilkinson, Johan Gustafsson, Finn Bacall, Khalid Belhajjame, Salvador Capella, José María Fernández González, Jacob Fosso Tande, Luiz Gadelha, Daniel Garijo, Patricia Grubel, Björn Grüning, Farah Zaib Khan, Sehrish Kanwal, Simone Leo, Stuart Owen, Luca Pireddu, Line Pouchard, Laura Rodriguez-Navas, Beatriz Serrano-Solano, Stian Soiland-Reyes, Baiba Vilne, Alan Williams, Merridee Ann Wouters, Frederik Coppens, Carole Goble
Date Published: 21st May 2025
Publication Type: InBook
DOI: 10.48550/arXiv.2505.15988
Citation:
Abstract (Expand)
Authors: Stian Soiland-Reyes, Peter Sefton, Simone Leo, Leyla Jael Castro, Claus Weiland, Herbert Van de Sompel
Date Published: 18th Mar 2025
Publication Type: Journal
Citation: Open Conf Proc 5
Abstract (Expand)
Authors: Abdulrahman Azab, Sanjay Kumar Srikakulam, Paul De Geest, Tomáš Vondrák, Björn Grüning, Mira Kuntz, Enol Fernandez-del-Castillo, Sebastian Luna-Valero
Date Published: 27th Feb 2025
Publication Type: Tech report
Citation: https://doi.org/10.5281/zenodo.15827107
Abstract (Expand)
Authors: Stian Soiland-Reyes, Eli Chadwick, Armin Dadras, Björn Grüning, Catalin Condurache, Sebastian Luna-Valero, Volodymyr Savchenko
Date Published: 8th Feb 2025
Publication Type: Tech report
Citation:
Abstract (Expand)
Authors: Abdulrahman Azab, Paul De Geest, Sanjay Kumar Srikakulam, Tomáš Vondra, Mira Kuntz, Björn Grüning
Date Published: 1st Feb 2025
Publication Type: Unpublished
Citation: https://doi.org/10.5281/zenodo.14936846
Abstract (Expand)
Authors: Simone Leo, Michael R. Crusoe, Laura Rodríguez-Navas, Raül Sirvent, Alexander Kanitz, Paul De Geest, Rudolf Wittner, Luca Pireddu, Daniel Garijo, José M. Fernández, Iacopo Colonnelli, Matej Gallo, Tazro Ohta, Hirotaka Suetake, Salvador Capella-Gutierrez, Renske de Wit, Bruno P. Kinoshita, Stian Soiland-Reyes
Date Published: 10th Sep 2024
Publication Type: Journal
DOI: 10.1371/journal.pone.0309210
Citation: PLoS ONE 19(9):e0309210
Abstract (Expand)
Authors: Stian Soiland-Reyes, Eli Chadwick, Finn Bacall, Jose M. Fernandez, Björn Grüning, Hakan Bayındır
Date Published: 28th Aug 2024
Publication Type: Tech report
Citation:
Abstract (Expand)
Authors: Stefano Nicotri, Marco Antonio Tangaro, Federico Zambelli, Miroslav Ruda, Ales Krenek, Björn Grüning, Sanjay Kumar Srikakulam, Anthony Bretaudeau, Sondre Batalden, María Chavero Díez, Paul De Geest
Date Published: 27th Aug 2024
Publication Type: Journal
Citation: https://doi.org/10.5281/zenodo.15920451
Abstract (Expand)
Authors: Maiken Pedersen, Sanjay Kumar Srikakulam, Paul De Geest, Enol Fernandez-del-Castillo, Andrea Cristofori, Sebastian Luna-Valero, Marco Antonio Tangaro, Stefano Nicotri
Date Published: 26th Aug 2024
Publication Type: Tech report
Citation: https://doi.org/10.5281/zenodo.15729502
Abstract (Expand)
Authors: Stian Soiland-Reyes, Björn Grüning, Paul De Geest
Date Published: 29th Feb 2024
Publication Type: Tech report
Citation: https://doi.org/10.5281/zenodo.10728922
Abstract (Expand)
Author: Vazov Nikolay
Date Published: 29th Feb 2024
Publication Type: Journal
Citation: https://doi.org/10.5281/zenodo.15826941
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 ...
Creators: Nick Juty, Finn Bacall
Submitter: Stian Soiland-Reyes
Presented at Swedish eResearch Centre meeting, 13 may 2022
Creator: Carole Goble
Submitter: Carole Goble
Keynote JOBIM 2021 (French Bioinformatics Conference)
FAIR Computational Workflows https://jobim2021.sciencesconf.org/ 8 July 2021
Computational workflows capture precise descriptions of the steps and data dependencies needed to carry out computational data pipelines, analysis and simulations in many areas of Science, including the Life Sciences. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for ...
Creator: Carole Goble
Submitter: Carole Goble
EOSC-Life FAIR hackathon 2021 Session 3: Workflow & Tools FAIRification
Creators: Carole Goble, Stuart Owen, Simone Leo, Finn Bacall, Stian Soiland-Reyes, Douglas Lowe
Submitter: Carole Goble
So, you want to build a pan-national digital space for bioscience data and methods? That works with a bunch of pre-existing data repositories and processing platforms? So you can share FAIR workflows and move them between services? Package them up with data and other stuff (or just package up data for that matter)? How? WorkflowHub (https://workflowhub.eu) and RO-Crate Research Objects (https://www.researchobject.org/ro-crate) that’s how! A step towards FAIR Digital Objects gets a workout. Keynote ...
Creator: Carole Goble
Submitter: Carole Goble
Keynote presented at WORKS 2021 https://works-workshop.org/
16th Workshop on Workflows in Support of Large-Scale Science November 15, 2021 Held in conjunction with SC21: The International Conference for High Performance Computing, Networking, Storage and Analysis
Creator: Carole Goble
Submitter: Carole Goble
Keynote at German Conference on Bioinformatics 2021 https://gcb2021.de/ FAIR Computational Workflows Computational workflows capture precise descriptions of the steps and data dependencies needed to carry out computational data pipelines, analysis and simulations in many areas of Science, including the Life Sciences. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for scalable data processing, the ...
Creator: Carole Goble
Submitter: Carole Goble
invited presentation at https://researchsoft.github.io/FAIReScience/, FAIReScience 2021 online workshop virtually co-located with the 17th IEEE International Conference on eScience (eScience 2021)
20th Sept 2021
Creator: Carole Goble
Submitter: Carole Goble
Keynote Presented at the ICTeSSH 2021 Conference to Social Science and Humanities. ICTeSSH 2021, 30th June 2021
https://ictessh.uns.ac.rs/ In data intensive science multi-step tool-chains are widely used to help scientists manage, analyze, and share increasing volumes of complex data. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for scalable data processing, the exchange of processing know-how, and ...
Creator: Carole Goble
Submitter: Carole Goble
EOSC-Life 3rd Open Call Biohackathon induction workshop
Start Date: 16th Dec 2021
End Date: 16th Dec 2021
Event Website: https://docs.google.com/document/d/1Ks7mf7xVLdnP4vLWj0zcJ2dvOXWtQyAu/edit
Country: Not specified
City: Virtual
Reproducibility is a cornerstone of good scientific practice. Thanks to funding provided by ELIXIR Training Platform Task 2, we have brought together the biggest names in bioinformatics workflow management for a 3 day practical workshop. We have presentations from the development teams of CWL, Snakemake, Nextflow, nf-core and more. If you want to learn more about the workflow management concepts that will be addressed in this workshop, check out these articles:
Workflow systems turn raw data into ...
Start Date: 29th Nov 2021
End Date: 1st Dec 2021
Event Website: https://elixir-workflow-workshop.github.io/2021/
Country: Germany
City: Virtual
virtually co-located with the 17th IEEE International Conference on eScience (eScience 2021)
This discussion-focused workshop examines how the FAIR (Findable, Accessible, Interoperable, Reusable) principles are and can be applied to eScience research objects beyond data. Invited speakers will present the idea of FAIR and its application to objects such as software, workflows, machine learning models, and executable notebooks, and where FAIR is going. Invited talks will be followed by a panel ...
Start Date: 20th Sep 2021
End Date: 20th Sep 2021
Event Website: https://researchsoft.github.io/FAIReScience/
Country: Not specified
City: Virtual
The public and the press already expect to assess the trustworthiness of research relevant to pressing social and public health issues in terms of transparency. While widely recognized as a critical component of research reproducibility in principle, the promise of making research fully transparent—and scientific claims easier to evaluate—via reliable provenance has yet to be realized in full. In particular, it is still far from routine for researchers in the natural, social, and data sciences ...
Start Date: 22nd Jul 2021
End Date: 22nd Jul 2021
Event Website: https://iitdbgroup.github.io/ProvenanceWeek2021/t7.html
Country: United States
City: Virtual
The FAIR Principles have two aspects: They were written specifically for research data and they also claim to be general for all research objects. In practice, this means that while the high-level concepts (findable, accessible, interoperable, and reusable) are generally applicable, the details of the wording, their context, and how they are applied is not. Different groups have been studying how the FAIR principles could be applied to other types of research objects, such as research software, ...
Start Date: 22nd Jun 2021
End Date: 22nd Jun 2021
Event Website: https://www.go-fair.org/events/fair-festival-2021/
Country: Not specified
City: Virtual
Date: Friday 11 June 2021, 10.00 CEST
Chairs: Carole Goble, Stian Soiland-Reyes, Salvador Capella-Gutiérrez, José María Fernández González and Frederik Coppens
In Life Sciences, experimental laboratory procedures usually have a lifespan since their first inception, wide adoption along the years, and later being superseded by others. The same applies to the analysis of the generated experimental data. Workflow Lifecycle represents the different states of workflows during their “life”. This workshop ...
Start Date: 11th Jun 2021
End Date: 11th Jun 2021
Event Website: https://docs.google.com/document/d/1AOE9jLO5EbUFu9NTe0B-z_jx8eQGIMSySkMLRMYvXO0/edit#heading=h.podt37y5jukq
Country: Not specified
City: Virtual
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 ...
Start Date: 30th Nov 2020
End Date: 30th Nov 2020
Event Website: https://conference.codata.org/FAIRconvergence2020/sessions/218/
Country: Not specified
City: Virtual
In the age of computational science, researchers in the life sciences – just as in other domains – regularly face the need of composing several individual software tools into pipelines or workflows that perform the specific data analysis processes that they need in their research. For over 20 years now, dedicated scientific workflow management systems have been supporting scientists in this task, and they continue to gain popularity. In fact, recent years have seen significant progress in the ...
Start Date: 7th Mar 2020
End Date: 13th Mar 2020
Event Website: https://www.lorentzcenter.nl/automated-workflow-composition-in-the-life-sciences.html
Country: Netherlands
City: Leiden
The results of the mentimeter for the FAIR workflows section of the EOSC-Life 3rd Open Call projects pre-hackathon induction
Creators: Carole Goble, Stian Soiland-Reyes, Stuart Owen, Finn Bacall, Simone Leo, Douglas Lowe
Submitter: Carole Goble
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.
Type: Snakemake
Creators: Alexander Hambley, Oliver Woolland, Eli Chadwick, Volodymyr Savchenko, José Mª Fernández, Stian Soiland-Reyes
Submitter: Eli Chadwick
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.
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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 ...
Type: Galaxy
Creators: Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet
Submitter: GTN Bot
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 ...
Type: Galaxy
Creators: Anthony Bretaudeau, Alexandre Cormier, Laura Leroi, Erwan Corre, Stéphanie Robin, Jonathan Kreplak
Submitters: GTN Bot, Armin Dadras
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.
Maintainers: Stian Soiland-Reyes, Paul De Geest, Eli Chadwick, Armin Dadras
Number of items: 48
Tags: Not specified
Workflows developed by or used by BY-COVID project.