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CORDIScovery podcast 50th episode CORDIScovery podcast 50th episode

leveraging the European compute infrastructures for data-intensive research guided by FAIR principles

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Documents, reports (3)
EuroScienceGateway data management and contingency management plan (opens in new window)

A data management plan (DMP) will be developed for the project, taking ethical and legal compliance measures into account, and incorporate all relevant project components from each work package. The DMP will evolve during the project and will be constantly updated. The consortium will enforce the use of open source licensed tools, packages and libraries, following the OSI recommendations. All scientific publications will be published Open Access and generated artefacts (tools, workflows), as well as services will be registered in EOSC supported registries.

Dissemination and exploitation plan (opens in new window)

A dissemination and exploitation plan will be developed in the first months of the project and execute a communication strategy, including:●Develop and update the project website.●Blog regularly on the consortium website as well as through the channels of the consortium partners to reach out to all stakeholders.●Participate in user conferences.●Make use of well established community channels in Twitter and other social media to share relevant news, use cases and other novelties.●Fostering community building by identifying and promoting user success stories, e.g. achievements, papers that have been enabled by EuroScienceGateway.

Community onboarding cookbook published (opens in new window)

Publication of Community onboarding cookbook

Publications

Other (75)
Connecting Galaxy to a compute cluster

Author(s): Nate Coraor, Björn Grüning, Helena Rasche
Published in: 2025
Publisher: Galaxy Training Materials

FAIR and Scalable Education (opens in new window)

Author(s): Anika Erxleben-Eggenhofer,Bérénice Batut,Teresa Müller
Published in: 2023
Publisher: TIB
DOI: 10.52825/CORDI.V1I.422

BioHackEU22 Report: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates (opens in new window)

Author(s): Ignacio Eguinoa, Marek Suchánek, Vojtěch Knaisl, Jan Slifka, Paul De Geest, David López, Björn Grüning, Simone Leo, Stian Soiland-Reyes
Published in: BioHackrXiv, 2023
Publisher: BioHackrXiv
DOI: 10.37044/OSF.IO/24JST

Optimized meta-scheduling in Galaxy using TPV Broker (opens in new window)

Author(s): Azab, Abdulrahman; De Geest, Paul; Srikakulam, Sanjay Kumar; Vondra, Tomáš; Kuntz, Mira; Grüning, Björn
Published in: 2025
Publisher: Zenodo
DOI: 10.5281/ZENODO.14936846

A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy

Author(s): Anup Kumar
Published in: 2025
Publisher: Galaxy Training Materials

Genome annotation with Braker3

Author(s): Romane LIBOUBAN, Anthony Bretaudeau
Published in: 2025
Publisher: Galaxy Training Materials

F1000 Research (opens in new window)

Author(s): Anthony Bretaudeau, Helena Rasche
Published in: 2023, ISSN 2046-1402
Publisher: F1000 Research Ltd.
DOI: 10.7490/F1000RESEARCH.1119590.1

EuroScienceGateway D2.2: Publishing workflow enriched FDOs to EOSC (opens in new window)

Author(s): Soiland-Reyes, Stian; Chadwick, Eli; Dadras, Armin; Grüning, Björn; Condurache, Catalin; Luna-Valero, Sebastian; Savchenko, Volodymyr
Published in: 2025
Publisher: Zenodo
DOI: 10.5281/zenodo.15094824

RO-Crate in Python

Author(s): Simone Leo, Bruno P. Kinoshita
Published in: 2023
Publisher: Galaxy Training Materials

Optimized meta-scheduling in Galaxy using TPV Broker (opens in new window)

Author(s): Azab, Abdulrahman; De Geest, Paul; Srikakulam, Sanjay Kumar; Vondra, Tomáš; Kuntz, Mira; Grüning, Björn
Published in: 2025
Publisher: Zenodo
DOI: 10.5281/ZENODO.14936846

Setting up Celery Workers for Galaxy

Author(s): Mira Kuntz
Published in: 2023
Publisher: Galaxy Training Materials

The Galaxy platform: Applications to catalysis workflows (opens in new window)

Author(s): Liborio L, Devadasan S, Austin P and Nieva de la Hidalga A.
Published in: 2024, ISSN 2046-1402
Publisher: F1000Research LTd
DOI: 10.7490/F1000RESEARCH.1119782.1

Setting up a dev Onedata instance

Author(s): Łukasz Opioła
Published in: 2025
Publisher: Galaxy Training Materials

Galaxy Sustainability Report (opens in new window)

Author(s): Jain, Smitesh
Published in: 2025
Publisher: Zenodo
DOI: 10.5281/ZENODO.16030328

Galaxy Interactive Tools

Author(s): Nate Coraor, Simon Gladman, Helena Rasche, Anthony Bretaudeau, José Manuel Domínguez
Published in: 2020
Publisher: Galaxy Training Materials

EuroScienceGateway: WP2 introduction (opens in new window)

Author(s): Soiland-Reyes, Stian; Goble, Carole
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7152762

Sharing data as machine-actionable objects using RO-Crate, Bioschemas and Signposting (opens in new window)

Author(s): Stian Soiland-Reyes; Simone Leo; Leyla Jael Castro; Peter Sefton; Carole Goble
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/ZENODO.7989657

WorkflowHub Knowledge Graph (opens in new window)

Author(s): Hambley, A., Chadwick, E., Woolland, O., Soiland-Reyes, S., & Savchenko, V.
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.13362051

Computing Simulations for Large Scale Experiments: the Case of Muons (opens in new window)

Author(s): Liborio, Leandro; Austin, Patrick; Beltran, Alejandra Gonzalez; Davies, Joel
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8161368

Introduction to deep learning

Author(s): Anup Kumar, Alireza Khanteymoori
Published in: 2025
Publisher: Galaxy Training Materials

Community onboarding cookbook published (opens in new window)

Author(s): Nikolay, Vazov
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.15826940

Onedata user-owned storage

Author(s): Łukasz Opioła, Bartosz Walkowicz
Published in: 2025
Publisher: Galaxy Training Materials

Comparison of two annotation tools - Helixer and Braker3

Author(s): Romane LIBOUBAN
Published in: 2025
Publisher: Galaxy Training Materials

Functional annotation of protein sequences

Author(s): Anthony Bretaudeau
Published in: 2022
Publisher: Galaxy Training Materials

Creating lightweight FAIR Digital Objects with RO-Crate and FAIR Signposting (opens in new window)

Author(s): Soiland-Reyes, Stian; Sefton, Peter; Castro, Leyla Jael; Coppens, Frederik; Garijo, Daniel; Leo, Simone; Portier, Marc; Groth, Paul; Goble, Carole
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/ZENODO.7245315

Genome annotation with Helixer

Author(s): Romane LIBOUBAN, Anthony Bretaudeau
Published in: 2025
Publisher: Galaxy Training Materials

FAIR-IMPACT synergies with EOSC4Cancer (opens in new window)

Author(s): Stian Soiland-Reyes; Carole Goble; Raquel Villodres Toledo; Romina Royo; Salvador Capella-Gutierrez
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6767548

EuroScienceGateway: WP2 introduction (opens in new window)

Author(s): Stian Soiland-Reyes; Carole Goble
Published in: EOSC, 2022
Publisher: EOSC
DOI: 10.5281/zenodo.7152762

Exporting to Onedata remote

Author(s): Łukasz Opioła, Bartosz Walkowicz
Published in: 2025
Publisher: Galaxy Training Materials

Publication on the smart job scheduler implementation (opens in new window)

Author(s): Azab, Abdulrahman; Srikakulam, Sanjay Kumar; De Geest, Paul; Vondrák, Tomáš; Grüning, Björn; Kuntz, Mira; Fernandez-del-Castillo, Enol; Luna-Valero, Sebastian
Published in: 2025
Publisher: Zenodo
DOI: 10.5281/ZENODO.15827107

Improving Galaxy provenance export using RO-Crate (opens in new window)

Author(s): De Geest, Paul; Coppens, Frederik; Eguinoa, Ignacio; Soiland-Reyes, Stian; Leo, Simone
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/ZENODO.7257145

Automating Galaxy workflows using the command line

Author(s): Simon Bray, Wolfgang Maier
Published in: 2025
Publisher: Galaxy Training Materials

EuroScienceGateway D2.1: Reproducible FAIR Digital Objects for Workflows (opens in new window)

Author(s): Soiland-Reyes, Stian; Chadwick, Eli; Bacall, Finn; Fernández, José M.; Grüning, Björn; Bayındır, Hakan
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.13225792

Analyse Argo data

Author(s): Marie Josse
Published in: 2025
Publisher: Galaxy Training Materials

Single-cell ATAC-seq standard processing with SnapATAC2

Author(s): Timon Schlegel
Published in: 2025
Publisher: Galaxy Training Materials

Configuring the Onedata connectors (remotes, Object Store, BYOS, BYOD)

Author(s): Łukasz Opioła, Bartosz Walkowicz
Published in: 2025
Publisher: Galaxy Training Materials

Make your tools available on your subdomain

Author(s): Marie Josse
Published in: 2024
Publisher: Galaxy Training Materials

From NDVI data with OpenEO to time series visualisation with Holoviews

Author(s): Marie Josse
Published in: 2024
Publisher: Galaxy Training Materials

Use Apptainer containers for running Galaxy jobs

Author(s): Torfinn Nome, Marius van den Beek, Matthias Bernt, Helena Rasche, Mira Kuntz
Published in: 2025
Publisher: Galaxy Training Materials

Importing (uploading) data from Onedata

Author(s): Łukasz Opioła, Bartosz Walkowicz
Published in: 2025
Publisher: Galaxy Training Materials

Galaxy Installation with Ansible

Author(s): Helena Rasche, Nate Coraor, Simon Gladman
Published in: 2019
Publisher: Galaxy Training Materials

Create a subdomain for your community on UseGalaxy.eu

Author(s): Marie Josse
Published in: 2024
Publisher: Galaxy Training Materials

Bring Your Own Infrastructure (opens in new window)

Author(s): Pedersen, Maiken; Srikakulam, Sanjay Kumar; De Geest, Paul; Fernandez-del-Castillo, Enol; Cristofori, Andrea; Luna-Valero, Sebastian; Tangaro, Marco Antonio; Nicotri, Stefano
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.15729502

Customizing the look of Galaxy

Author(s): Laila Los
Published in: 2023
Publisher: Galaxy Training Materials

Marine Omics identifying biosynthetic gene clusters

Author(s): Marie Josse
Published in: 2024
Publisher: Galaxy Training Materials

Galaxy and Scientific Communities: How to Incorporate New Ones, Uplift Engaged Ones and Maintain Mature Ones (opens in new window)

Author(s): Liborio, L.; P. Austin; A. Gonzalez-Beltran; E. Chadwick; V. Savchenko; A. Neronov; J. Iaquinta; A. Bretaudeau
Published in: Conference: PASC2023 , Davos, Switzerland, 26-27 June 2023, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8114821

Masking repeats with RepeatMasker

Author(s): Anthony Bretaudeau, Alexandre Cormier, Laura Leroi, Erwan Corre, Stéphanie Robin, Jonathan Kreplak
Published in: 2021
Publisher: Galaxy Training Materials

Genome annotation with Helixer

Author(s): Romane LIBOUBAN, Anthony Bretaudeau
Published in: 2025
Publisher: Galaxy Training Materials

Best practices for workflows in GitHub repositories

Author(s): Simone Leo, Eli Chadwick
Published in: 2023
Publisher: Galaxy Training Materials

Interactive Tools (IT) in Galaxy (opens in new window)

Author(s): Kayikcioglu, Tunc; Srikakulam, Sanjay Kumar; Maier, Wolfgang; Grüning, Björn
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/ZENODO.8335099

Running Jobs on Remote Resources with Pulsar

Author(s): Nate Coraor, Simon Gladman, Marius van den Beek, Helena Rasche, Gianmauro Cuccuru, Mira Kuntz
Published in: 2025
Publisher: Galaxy Training Materials

Getting your hands-on earth data

Author(s): Marie Josse
Published in: 2024, Page(s) GALAXY TRAINING
Publisher: Galaxy Training Materials

Enabling an operational, open and FAIR EOSC ecosystem (opens in new window)

Author(s): Sebastian Schaaf,Anika Erxleben-Eggenhofer, Björn Grüning, The EuroScienceGateway Project
Published in: 2023
Publisher: ELIXIR
DOI: 10.7490/F1000RESEARCH.1119627.1

RO-Crate - Introduction

Author(s): Stian Soiland-Reyes, Peter Sefton
Published in: 2023
Publisher: Galaxy Training Materials

Refining Genome Annotations with Apollo (eukaryotes)

Author(s): Anthony Bretaudeau
Published in: 2025
Publisher: Galaxy Training Materials

The Galaxy Platform and its Applications to Materials Science (opens in new window)

Author(s): Liborio, Leandro; Gonzalez-Beltran, Alejandra; Austin, Patrick; Chadwick, Eli
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8161429

Interactive Tools (IT) in Galaxy (opens in new window)

Author(s): Tunc Kayikcioglu University of Freiburg,Sanjay Kumar Srikakulam University of Freiburg, Wolfgang Maier University of Freiburg ,Björn Grüning University of Freiburg
Published in: 2023
Publisher: TIB
DOI: 10.52825/CORDI.V1I.419

EuroScienceGateway Data Management Plan (DMP; D1.1) (opens in new window)

Author(s): Erxleben, Anika; Schaaf, Sebastian; D'Anna, Flora; Gruening, Bjoern; Coppens, Frederik
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/ZENODO.10054550

EuroscienceGateway Dissemination & Exploitation plan (D&E; D1.2) (opens in new window)

Author(s): Erxleben, Anika; Schaaf, Sebastian; Marchis, Oana; Gruening, Bjoern
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.10055554

Making Earth System Modelling and Observation Workflows Reproducible and Portable Across Federated High-Performance Computer and Cloud Platforms with Conda-based Containers (opens in new window)

Author(s): Iaquinta, Jean; Fouilloux, Anne
Published in: 2025
Publisher: Zenodo
DOI: 10.5281/ZENODO.15600666

Galaxy Database schema

Author(s): Hans-Rudolf Hotz, Björn Grüning
Published in: 2016
Publisher: Galaxy Training Materials

Finding the muon stopping site with pymuon-suite in Galaxy

Author(s): Leandro Liborio, Eli Chadwick, Patrick Austin
Published in: 2024
Publisher: Galaxy Training Materials

Refining Genome Annotations with Apollo (prokaryotes)

Author(s): Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet
Published in: 2021
Publisher: Galaxy Training Materials

Getting started with Onedata distributed storage

Author(s): Łukasz Opioła, Bartosz Walkowicz
Published in: 2025
Publisher: Galaxy Training Materials

Creating high resolution images of Galaxy Workflows

Author(s): Laila Los
Published in: 2024
Publisher: Galaxy Training Materials

Ocean Data View (ODV)

Author(s): Marie Josse
Published in: 2023
Publisher: Galaxy Training Materials

EuroScienceGateway MS3: Initial EuroScienceGateway workflows registered (opens in new window)

Author(s): Soiland-Reyes, Stian; Grüning, Björn; De Geest, Paul
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.10728922

EuroScienceGateway D2.1: Reproducible FAIR Digital Objects for Workflows (opens in new window)

Author(s): Soiland-Reyes, Stian; Chadwick, Eli; Bacall, Finn; Fernández, José M.; Grüning, Björn; Bayındır, Hakan
Published in: Soiland-Reyes , S , Chadwick , E , Bacall , F , Fernández , J M , Grüning , B & Bayındır , H 2024 , EuroScienceGateway D2.1: Reproducible FAIR Digital Objects for Workflows . Zenodo . https://doi.org/10.5281/zenodo.13225792, 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.13225792

Genome Annotation

Author(s): Anika Erxleben, Björn Grüning
Published in: 2015
Publisher: Galaxy Training Materials

Ocean's variables study

Author(s): Marie Josse
Published in: 2025
Publisher: Galaxy Training Materials

Sentinel 5P data visualisation

Author(s): Marie Josse
Published in: 2024
Publisher: Galaxy Training Materials

Genome annotation with Funannotate

Author(s): Anthony Bretaudeau
Published in: 2023
Publisher: Galaxy Training Materials

D3.1 Operations documentation on the Open Infrastructure deployment (opens in new window)

Author(s): Nicotri, Stefano; Tangaro, Marco Antonio; Zambelli, Federico; Ruda, Miroslav; Krenek, Ales; Grüning, Björn; Srikakulam, Sanjay Kumar; Bretaudeau, Anthony; Batalden, Sondre; Chavero Díez, María; De Geest, Paul
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.15920451

Obis marine indicators

Author(s): Marie Josse, Yvan Le Bras
Published in: 2023
Publisher: Galaxy Training Materials

The Galaxy Platform: Applications to Catalysis Workflows (opens in new window)

Author(s): P. Austin; A. Gonzalez-Beltran; A. Nieva De La Hidalga; Liborio, L.
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8114859

Peer reviewed articles (28)
Evaluating FAIR Digital Object and Linked Data as distributed object systems (opens in new window)

Author(s): Stian Soiland-Reyes, Carole Goble, Paul Groth
Published in: arXiv, 2023
Publisher: CORNELL UNIVERSITY
DOI: 10.48550/arXiv.2306.07436

Conda, Container and Bots (opens in new window)

Author(s): Zierep, Paul; Srikakulam, Sanjay Kumar; Schaaf, Sebastian; Grüning, Björn
Published in: Proceedings of the Conference on Research Data Infrastructure, 2023, ISSN 2941-296X
Publisher: TIB Open Publishing (Technische Informationsbibliothek (TIB)) on behalf of Nationale Forschungsdateninfrastruktur (NFDI) e.V.
DOI: 10.52825/CORDI.V1I.417

Dynamic configuration and data security for bioinformatics cloud services with the Laniakea Dashboard (opens in new window)

Author(s): Marco Antonio Tangaro; Marica Antonacci; Giacinto Donvito; Nadina Foggetti; Pietro Mandreoli; Daniele Colombo; Graziano Pesole; Federico Zambelli
Published in: NAR Genomics and Bioinformatics, Issue 4, 2024, ISSN 2631-9268
Publisher: Oxford University Press
DOI: 10.1093/NARGAB/LQAE140

RO-Crate: packaging metadata love notes into FAIR Digital Objects (opens in new window)

Author(s): Carole Goble, Stian Soiland-Reyes
Published in: Helmholtz Metadata Collaboration | Conference 2022, 2022
Publisher: HMC
DOI: 10.5281/zenodo.7147703

Galaxy Training: A powerful framework for teaching! (opens in new window)

Author(s): Hiltemann, S., Rasche, H., Gladman, S., Hotz, H.-R., Larivière, D., Blankenberg, D., Jagtap, P. D., Wollmann, T., Bretaudeau, A., Goué, N., Griffin, T. J., Royaux, C., Le Bras, Y., Mehta, S., Syme, A., Coppens, F., Droesbeke, B., Soranzo, N., Bacon, W., P
Published in: PLoS Computational Biology, Issue 1, 2023, ISSN 1544-9173
Publisher: Public Library of Science
DOI: 10.1371/JOURNAL.PCBI.1010752

WorkflowHub: a registry for computational workflows (opens in new window)

Author(s): 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
Published in: Scientific Data, Issue 12, 2025, ISSN 2052-4463
Publisher: Nature
DOI: 10.1038/S41597-025-04786-3

Integrative meta-omics in Galaxy and beyond (opens in new window)

Author(s): Valerie C. Schiml,Francesco Delogu,Praveen Kumar,Benoit Kunath,Bérénice Batut,Subina Mehta,James E. Johnson,Björn Grüning,Phillip B. Pope,Pratik D. Jagtap,Timothy J. Griffin,Magnus Ø. Arntzen
Published in: Environmental Microbiome, 2023, ISSN 2524-6372
Publisher: BMC
DOI: 10.1186/s40793-023-00514-9

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond (opens in new window)

Author(s): Simon Bray, John Chilton, Matthias Bernt, Nicola Soranzo, Marius van den Beek, Bérénice Batut, Helena Rasche, Martin Čech, Peter J A Cock, Björn Grüning, Anton Nekrutenko
Published in: Genome Research, Issue 2, 2023, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/GR.276963.122

Facilitating Reproducibility in Catalysis Research with Managed Workflows and RO‐Crates: A Galaxy Case Study (opens in new window)

Author(s): Abraham Nieva‐de‐la‐Hidalga, Leandro Liborio, Patrick Austin, Subindev Devadasan, Tom Underwood, Alexander Belozerov, Martin Wilding, Nitya Ramanan, C. Richard A. Catlow
Published in: ChemCatChem, Issue 17, 2025, ISSN 1867-3880
Publisher: Wiley
DOI: 10.1002/CCTC.202401676

PLoS ONE (opens in new window)

Author(s): 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
Published in: PLOS ONE, 2024, ISSN 1932-6203
Publisher: PLOS ONE
DOI: 10.48550/arxiv.2312.07852

Training Infrastructure as a Service (opens in new window)

Author(s): Helena Rasche,Cameron Hyde,John Davis,Simon Gladman,Nate Coraor,Anthony Bretaudeau,Gianmauro Cuccuru,Wendi Bacon,Beatriz Serrano-Solano,Jennifer Hillman-Jackson,Saskia Hiltemann,Miaomiao Zhou,Björn Grüning,Andrew Stubbs
Published in: Gigascience, 2023, ISSN 2047-217X
Publisher: Oxford University Press
DOI: 10.1093/gigascience/giad048

Establishing the ELIXIR Microbiome Community (opens in new window)

Author(s): Robert D. Finn, Bachir Balech, Josephine Burgin, Physilia Chua, Erwan Corre, Cymon J. Cox, Claudio Donati, Vitor Martins dos Santos, Bruno Fosso, John Hancock, Katharina F. Heil, Naveed Ishaque, Varsha Kale, Benoit J. Kunath, Claudine Médigue, Evangelos Pafilis, Graziano Pesole, Lorna Richardson, Monica Santamaria, Tim Van Den Bossche, Juan Antonio Vizcaíno, Haris Zafeiropoulos, Nils P. Willassen, Eric Pelletier, Bérénice Batut
Published in: F1000Research, Issue 13, 2024, ISSN 2046-1402
Publisher: F1000 Research Ltd
DOI: 10.12688/F1000RESEARCH.144515.1

Finding workflows in the Galaxy universe: integrating a global ecosystem using workflow registries (opens in new window)

Author(s): Gustafsson, Ove Johan Ragnar; Soranzo, Nicola; Gruening, Bjoern; van den Beek, Marius; Bacall, Finn; Goble, Carole; Zaib Khan, Farah; Price, Gareth; Ward, Nigel; Christiansen, Jeff
Published in: GALAXY AUSTRALIA, 2023
Publisher: GALAXY AUSTRALIA
DOI: 10.5281/zenodo.8157531

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses (opens in new window)

Author(s): Nadim Rahman, Colman O'Cathail, Ahmad Zyoud, Alexey Sokolov, Bas Oude Munnink, Björn Grüning, Carla Cummins, Clara Amid, David F. Nieuwenhuijse, Dávid Visontai, David Yu Yuan, Dipayan Gupta, Divyae K. Prasad, Gábor Máté Gulyás, Gabriele Rinck, Jasmine McKinnon, Jeena Rajan, Jeff Knaggs, Jeffrey Edward Skiby, József Stéger, Judit Szarvas, Khadim Gueye, Krisztián Papp, Maarten Hoek, Manish Kumar, Marianna A. Ventouratou, Marie-Catherine Bouquieaux, Martin Koliba, Milena Mansurova, Muhammad Haseeb, Nathalie Worp, Peter W. Harrison, Rasko Leinonen, Ross Thorne, Sandeep Selvakumar, Sarah Hunt, Sundar Venkataraman, Suran Jayathilaka, Timothée Cezard, Wolfgang Maier, Zahra Waheed, Zamin Iqbal, Frank Møller Aarestrup, Istvan Csabai, Marion Koopmans, Tony Burdett, Guy Cochrane
Published in: Microbial Genomics, Issue 10, 2024, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/MGEN.0.001188

An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy (opens in new window)

Author(s): Anup Kumar, Gianmauro Cuccuru, Björn Grüning, Rolf Backofen
Published in: Gigascience, 2023, ISSN 2047-217X
Publisher: Oxford University Press
DOI: 10.1093/gigascience/giad028

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy (opens in new window)

Author(s): Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjorn Grüning, Byung June Ko, Alex Ostrovsky, Marc Palmada-Flores, Brandon D. Pickett, Keon Rabbani, Agostinho Antunes, Jennifer R. Balacco, Mark J. P. Chaisson, Haoyu Cheng, Joanna Collins, Melanie Couture, Alexandra Denisova, Olivier Fedrigo, Guido Roberto Gallo, Alice Maria Giani, Grenville MacDonald Gooder, Kathleen Horan, Nivesh Jain, Cassidy Johnson, Heebal Kim, Chul Lee, Tomas Marques-Bonet, Brian O’Toole, Arang Rhie, Simona Secomandi, Marcella Sozzoni, Tatiana Tilley, Marcela Uliano-Silva, Marius van den Beek, Robert W. Williams, Robert M. Waterhouse, Adam M. Phillippy, Erich D. Jarvis, Michael C. Schatz, Anton Nekrutenko, Giulio Formenti
Published in: Nature Biotechnology, Issue 42, 2024, ISSN 1087-0156
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41587-023-02100-3

Der europäische Galaxy-Server demokratisiert die Analyse biowissenschaftlicher Daten (opens in new window)

Author(s): Erxleben-Eggenhofer, Anika
Published in: Laborjournal, 2023, ISSN 1612-8354
Publisher: LJ-Verlag Herfort und Sailer
DOI: 10.3030/101057388

Evaluating FAIR Digital Object and Linked Data as distributed object systems (opens in new window)

Author(s): Stian Soiland-Reyes; Carole Goble; Paul Groth
Published in: PeerJ Computer Science, 2024, ISSN 2376-5992
Publisher: PeerJ Inc.
DOI: 10.48550/arxiv.2306.07436

Making workflow provenance FAIR across workflow systems with Workflow Run RO-Crate (opens in new window)

Author(s): Simone Leo; Laura Rodríguez-Navas; José M. Fernández; Paul De Geest; Luca Pireddu; Michael R. Crusoe; Daniel Garijo; Iacopo Colonnelli; Raül Sirvent; Stian Soiland-Reyes
Published in: F1000RESEARCH, 2023
Publisher: F1000RESEARCH
DOI: 10.5281/zenodo.8004793

Hydrogen Radical Chemistry at High-Symmetry {2Fe2S} Centers Probed Using a Muonium Surrogate (opens in new window)

Author(s): Joseph A. Wright, Farhana Haque, Leandro Liborio, Stephen P. Cottrell
Published in: Inorganic Chemistry, Issue 64, 2025, ISSN 0020-1669
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.INORGCHEM.4C05126

EuroScienceGateway: robust, scalable, and integrated open infrastructure for data-driven research within EOSC

Author(s): Volodymyr Savchenko
Published in: SKAO, 2023
Publisher: SKAO

Applying the FAIR Principles to computational workflows (opens in new window)

Author(s): 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
Published in: Scientific Data, Issue 1, 2025, ISSN 2052-4463
Publisher: Nature
DOI: 10.1038/S41597-025-04451-9

Inorganic Chemistry (opens in new window)

Author(s): Wright, Joseph A., Farhana Haque, Leandro Liborio, and Stephen P. Cottrell
Published in: Inorganic Chemistry, Issue 10, 2025, ISSN 0020-1669
Publisher: American Chemical Society
DOI: 10.1021/ACS.INORGCHEM.4C05126

DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data (opens in new window)

Author(s): Johanna Galvis, Joris Guyon, Benjamin Dartigues, Helge Hecht, Björn Grüning, Florian Specque, Hayssam Soueidan, Slim Karkar, Thomas Daubon, Macha Nikolski
Published in: Bioinformatics, Issue 40, 2024, ISSN 1367-4811
Publisher: Oxford University Press (OUP)
DOI: 10.1093/BIOINFORMATICS/BTAE282

Electronic structure calculations for muon spectroscopy<sup>*</sup> (opens in new window)

Author(s): Stephen J Blundell, Miki Bonacci, Pietro Bonfà, Roberto De Renzi, Benjamin M Huddart, Tom Lancaster, Leandro M Liborio, Ifeanyi J Onuorah, Giovanni Pizzi, Francis L Pratt, John M Wilkinson
Published in: Electronic Structure, Issue 7, 2025, ISSN 2516-1075
Publisher: IOP Publishing
DOI: 10.1088/2516-1075/ADCB7C

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (opens in new window)

Author(s): Linelle Ann L Abueg; Enis Afgan; Olivier Allart; Ahmed H Awan; Wendi A Bacon; Dannon Baker; Madeline Bassetti; Bérénice Batut; Matthias Bernt; Daniel Blankenberg; Aureliano Bombarely; Anthony Bretaudeau; Catherine J Bromhead; Melissa L Burke; Patrick K Capon; Martin Čech; María Chavero-Díez; John M Chilton; Tyler J Collins; Frederik Coppens; Nate Coraor; Gianmauro Cuccuru; Fabio Cumbo; John Davis; Paul F De Geest; Willem de Koning; Martin Demko; Assunta DeSanto; José Manuel Domínguez Begines; Maria A Doyle; Bert Droesbeke; Anika Erxleben-Eggenhofer; Melanie C Föll; Giulio Formenti; Anne Fouilloux; Rendani Gangazhe; Tanguy Genthon; Jeremy Goecks; Alejandra N Gonzalez Beltran; Nuwan A Goonasekera; Nadia Goué; Timothy J Griffin; Björn A Grüning; Aysam Guerler; Sveinung Gundersen; Ove Johan Ragnar Gustafsson; Christina Hall; Thomas W Harrop; Helge Hecht; Alireza Heidari; Tillman Heisner; Florian Heyl; Saskia Hiltemann; Hans-Rudolf Hotz; Cameron J Hyde; Pratik D Jagtap; Julia Jakiela; James E Johnson; Jayadev Joshi; Marie Jossé; Khaled Jum’ah; Matúš Kalaš; Katarzyna Kamieniecka; Tunc Kayikcioglu; Markus Konkol; Leonid Kostrykin; Natalie Kucher; Anup Kumar; Mira Kuntz; Delphine Lariviere; Ross Lazarus; Yvan Le Bras; Gildas Le Corguillé; Justin Lee; Simone Leo; Leandro Liborio; Romane Libouban; David López Tabernero; Lucille Lopez-Delisle; Laila S Los; Alexandru Mahmoud; Igor Makunin; Pierre Marin; Subina Mehta; Winnie Mok; Pablo A Moreno; François Morier-Genoud; Stephen Mosher; Teresa Müller; Engy Nasr; Anton Nekrutenko; Tiffanie M Nelson; Asime J Oba; Alexander Ostrovsky; Polina V Polunina; Krzysztof Poterlowicz; Elliott J Price; Gareth R Price; Helena Rasche; Bryan Raubenolt; Coline Royaux; Luke Sargent; Michelle T Savage; Volodymyr Savchenko; Denys Savchenko; Michael C Schatz; Pauline Seguineau; Beatriz Serrano-Solano; Nicola Soranzo; Sanjay Kumar Srikakulam; Keith Suderman; Anna E Syme; Marco Antonio Tangaro; Jonathan A Tedds; Mehmet Tekman; Wai Cheng (Mike) Thang; Anil S Thanki; Michael Uhl; Marius van den Beek; Deepti Varshney; Jenn Vessio; Pavankumar Videm; Greg Von Kuster; Gregory R Watson; Natalie Whitaker-Allen; Uwe Winter; Martin Wolstencroft; Federico Zambelli; Paul Zierep; Rand Zoabi
Published in: Nucleic Acids Research, 2024, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/NAR/GKAE410

An Ecosystem of Services for FAIR Computational Workflows (opens in new window)

Author(s): Sean R. Wilkinson, Johan Gustafsson, Finn Bacall, Khalid Belhajjame, Salvador Capella, Jose Maria Fernandez Gonzalez, Jacob Fosso Tande, Luiz Gadelha, Daniel Garijo, Patricia Grubel, Bjorn Grüning, Farah Zaib Khan, Sehrish Kanwal, Simone Leo, Stuart Owen,
Published in: Arxiv, Computer Science, Distributed, Parallel, and Cluster Computing, 2025, ISSN 2331-8422
Publisher: ArXiv
DOI: 10.48550/ARXIV.2505.15988

Recording provenance of workflow runs with RO-Crate (opens in new window)

Author(s): 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
Published in: PLOS ONE, Issue 19, 2024, ISSN 1932-6203
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/JOURNAL.PONE.0309210

Conference proceedings (21)
Making workflow provenance FAIR across workflow systems with Workflow Run RO-Crate (opens in new window)

Author(s): Leo, Simone; Rodríguez-Navas, Laura; Fernández, José M.; De Geest, Paul; Pireddu, Luca; Crusoe, Michael R.; Garijo, Daniel; Colonnelli, Iacopo; Sirvent, Raül; Soiland-Reyes, Stian
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8004793

Galaxy France: an example of a national UseGalaxy server (opens in new window)

Author(s): Siguret, Clea, Thomas Chaussepied, Romane Libouban, Eva Mercier, Julien Seiler, Bérénice Batut, Gildas Le Corguillé, and Anthony Bretaudeau
Published in: 2024
Publisher: Galaxy Community Conference
DOI: 10.7490/F1000RESEARCH.1119767.1

Computing Simulations for Large Scale Experiments: the Case of Muons

Author(s): Leandro Liborio; Patrick Austin; Alejandra Gonzalez Beltran; Joel Davies
Published in: 2023

Misconceptions about Galaxy debunked by the (French) Galaxy Community

Author(s): Romane Libouban, Eva Mercier, Thomas Chaussepied, Bérénice Batut, Anthony Bretaudeau, Gildas Le Corguillé
Published in: JOBIM 2024 - Journées Ouvertes Biologie Informatique Mathématiques, Jun 2024, TOULOUSE, France. pp.1-28., 2024
Publisher: HAL

Galaxy and RDM (opens in new window)

Author(s): Sebastian Schaaf, Anika Erxleben-Eggenhofer, Bjoern Gruening
Published in: Vol. 1 (2023): 1st Conference on Research Data Infrastructure (CoRDI) - Connecting Communities, 2023
Publisher: 1st Conference on Research Data Infrastructure
DOI: 10.52825/cordi.v1i.421

Breaking myths: The reality of Galaxy’s capabilities and impact

Author(s): Gildas Le Corguillé, Anthony Bretaudeau, Björn Grüning, Wendi Bacon, Bérénice Batut
Published in: JOBIM 2025 - Journées Ouvertes en bioinformatique et de la biostatistique francophone, Jul 2025, Bordeaux, France., 2025
Publisher: HAL

Dynamic meta-scheduling in Galaxy with TPV Broker for smarter workload distribution (opens in new window)

Author(s): Srikakulam, Sanjay Kumar; Azab, Abdulrahman; De Geest, Paul; Vondrák, Tomáš; Kuntz, Mira; Luna-Valero, Sebastian; Grüning, Björn
Published in: 2025
Publisher: Zenodo
DOI: 10.5281/ZENODO.16312226

Climate Modeling with Conda and Containers to Improve Computational Resource Usage while Achieving Native Performance and Reproducibility (opens in new window)

Author(s): Iaquinta, Jean; Fouilloux, Anne; Ragan-Kelley, Benjamin
Published in: Crossref, 2025
Publisher: Zenodo
DOI: 10.5281/ZENODO.15600119

Practical webby FDOs With RO-Crate and FAIR Signposting (opens in new window)

Author(s): Stian Soiland-Reyes; Peter Sefton; Simone Leo; Leyla Jael Castro; Claus Weiland; Herbert Van de Sompel
Published in: 2025
Publisher: TIB Open Publishing
DOI: 10.52825/OCP.V5I.1273

Climate Modeling with Conda and Containers to Improve Computational Resource Usage while Achieving Native Performance and Reproducibility (opens in new window)

Author(s): Jean Iaquinta, Anne Fouilloux, Benjamin Ragan-Kelley
Published in: 2025
Publisher: Copernicus GmbH
DOI: 10.5194/EGUSPHERE-EGU25-2605

Galaxy and Scientific Communities: How to Incorporate New Ones, Uplift Engaged Ones and Maintain Mature Ones (opens in new window)

Author(s): L. Liborio; P. Austin; A. Gonzalez-Beltran; E. Chadwick; V. Savchenko; A. Neronov; J. Iaquinta; A. Bretaudeau
Published in: PASC DAVOS, 2023
Publisher: PASC DAVOS
DOI: 10.5281/zenodo.8114821

MuonGalaxy - tools, workflows and more for muons and materials science (opens in new window)

Author(s): Austin, Patrick; Davies, Joel; Gonzalez-Beltran, Alejandra; Liborio, Leandro
Published in: GALAXY PROJECT, 2023
Publisher: GALAXY PROJEC
DOI: 10.5281/zenodo.8116071

Making EOSC Research Objects FAIR with RO-Crate: A common metadata overlay for EOSC repositories (opens in new window)

Author(s): Justin Clark-Casey; Stian Soiland-Reyes
Published in: EOSC, 2022
Publisher: EOSC
DOI: 10.5281/zenodo.7323480

Implementation of a reproducible pipeline for producing seasonal Arctic sea ice forecasts (opens in new window)

Author(s): Vanessa Stöckl, Björn Grüning, Anne Fouilloux, Jean Iaquinta, Alejandro Coca-Castro
Published in: 2024
Publisher: Copernicus GmbH
DOI: 10.5194/EGUSPHERE-EGU24-8343

Building a Distributed Computing Network for Galaxy, Application to Genome Annotation

Author(s): Eva Mercier, Romane Libouban, Thomas Chaussepied, Anthony Bretaudeau
Published in: Application to Genome Annotation. JOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. 2024., 2024
Publisher: HAL Open Science

Improving Galaxy provenance export using RO-Crate (opens in new window)

Author(s): Paul De Geest; Frederik Coppens; Ignacio Eguinoa; Stian Soiland-Reyes; Simone Leo
Published in: Research Ideas and Outcomes, 2022
Publisher: MANCHESTER 1824
DOI: 10.5281/zenodo.7257146

The Galaxy Platform and its Applications to Materials Science (opens in new window)

Author(s): Leandro Liborio; Alejandra Gonzalez-Beltran; Patrick Austin; Eli Chadwick
Published in: STFC, 2024
Publisher: GALAXY COMMUNITY HUB
DOI: 10.5281/zenodo.8161429

Using FAIR and Open Science practices to better understand vegetation browning in Troms and Finnmark (Norway) (opens in new window)

Author(s): Jean Iaquinta, Anne Fouilloux
Published in: EGU General Assembly 2023, 2023
Publisher: EGU General Assembly 2023
DOI: 10.5194/EGUSPHERE-EGU23-2579

Enhancing RDM in Galaxy by integrating RO-Crate (opens in new window)

Author(s): Paul De Geest; Frederik Coppens; Stian Soiland-Reyes; Ignacio Eguinoa; Simone Leo
Published in: Research Ideas and Outcomes, 2022
Publisher: Research Ideas and Outcomes
DOI: 10.3897/rio.8.e95164

Improving Galaxy provenance export using RO-Crate (opens in new window)

Author(s): De Geest, Paul; Coppens, Frederik; Eguinoa, Ignacio; Soiland-Reyes, Stian; Leo, Simone
Published in: 1st International Conference on FAIR Digital Objects (FDO2022) , Leiden, The Netherlands, 2022-10-26/--28, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7257146

Making EOSC Research Objects FAIR with RO-Crate: A common metadata overlay for EOSC repositories (opens in new window)

Author(s): Clark-Casey, Justin; Soiland-Reyes, Stian
Published in: EOSC Symposium 2022 , Prague, CZ, 2022-11-14/--17 (Session FAIR enabling practices, Part A), 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7323301

Book chapters (2)
Unlocking the Potential of Containers in Scientific Computing to Achieve Bitwise Reproducibility, Portability and Performance (opens in new window)

Author(s): Jean Iaquinta, Anne Fouilloux
Published in: Communications in Computer and Information Science, Nordic e-Infrastructure Tomorrow, 2024, ISSN 1865-0937
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-86240-3_4

Integration of Nordugrid ARC with Galaxy and EGI IM (opens in new window)

Author(s): Maiken Pedersen, Balazs Konya, Sebastian Luna-Valero, Björn Grüning
Published in: Communications in Computer and Information Science, Nordic e-Infrastructure Tomorrow, 2025
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-86240-3_5

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