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

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

EuroScienceGateway data management and contingency management plan

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

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

Publication of Community onboarding cookbook

Publicaciones

Connecting Galaxy to a compute cluster

Autores: Nate Coraor, Björn Grüning, Helena Rasche
Publicado en: 2025
Editor: Galaxy Training Materials

FAIR and Scalable Education

Autores: Anika Erxleben-Eggenhofer,Bérénice Batut,Teresa Müller
Publicado en: 2023
Editor: TIB
DOI: 10.52825/CORDI.V1I.422

BioHackEU22 Report: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates

Autores: Ignacio Eguinoa, Marek Suchánek, Vojtěch Knaisl, Jan Slifka, Paul De Geest, David López, Björn Grüning, Simone Leo, Stian Soiland-Reyes
Publicado en: BioHackrXiv, 2023
Editor: BioHackrXiv
DOI: 10.37044/OSF.IO/24JST

Optimized meta-scheduling in Galaxy using TPV Broker

Autores: Azab, Abdulrahman; De Geest, Paul; Srikakulam, Sanjay Kumar; Vondra, Tomáš; Kuntz, Mira; Grüning, Björn
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.14936846

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

Autores: Anup Kumar
Publicado en: 2025
Editor: Galaxy Training Materials

Genome annotation with Braker3

Autores: Romane LIBOUBAN, Anthony Bretaudeau
Publicado en: 2025
Editor: Galaxy Training Materials

F1000 Research

Autores: Anthony Bretaudeau, Helena Rasche
Publicado en: 2023, ISSN 2046-1402
Editor: F1000 Research Ltd.
DOI: 10.7490/F1000RESEARCH.1119590.1

EuroScienceGateway D2.2: Publishing workflow enriched FDOs to EOSC

Autores: Soiland-Reyes, Stian; Chadwick, Eli; Dadras, Armin; Grüning, Björn; Condurache, Catalin; Luna-Valero, Sebastian; Savchenko, Volodymyr
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/zenodo.15094824

RO-Crate in Python

Autores: Simone Leo, Bruno P. Kinoshita
Publicado en: 2023
Editor: Galaxy Training Materials

Optimized meta-scheduling in Galaxy using TPV Broker

Autores: Azab, Abdulrahman; De Geest, Paul; Srikakulam, Sanjay Kumar; Vondra, Tomáš; Kuntz, Mira; Grüning, Björn
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.14936846

Setting up Celery Workers for Galaxy

Autores: Mira Kuntz
Publicado en: 2023
Editor: Galaxy Training Materials

The Galaxy platform: Applications to catalysis workflows

Autores: Liborio L, Devadasan S, Austin P and Nieva de la Hidalga A.
Publicado en: 2024, ISSN 2046-1402
Editor: F1000Research LTd
DOI: 10.7490/F1000RESEARCH.1119782.1

Setting up a dev Onedata instance

Autores: Łukasz Opioła
Publicado en: 2025
Editor: Galaxy Training Materials

Galaxy Sustainability Report

Autores: Jain, Smitesh
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.16030328

Galaxy Interactive Tools

Autores: Nate Coraor, Simon Gladman, Helena Rasche, Anthony Bretaudeau, José Manuel Domínguez
Publicado en: 2020
Editor: Galaxy Training Materials

EuroScienceGateway: WP2 introduction

Autores: Soiland-Reyes, Stian; Goble, Carole
Publicado en: 2022
Editor: Zenodo
DOI: 10.5281/zenodo.7152762

Sharing data as machine-actionable objects using RO-Crate, Bioschemas and Signposting

Autores: Stian Soiland-Reyes; Simone Leo; Leyla Jael Castro; Peter Sefton; Carole Goble
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/ZENODO.7989657

WorkflowHub Knowledge Graph

Autores: Hambley, A., Chadwick, E., Woolland, O., Soiland-Reyes, S., & Savchenko, V.
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.13362051

Computing Simulations for Large Scale Experiments: the Case of Muons

Autores: Liborio, Leandro; Austin, Patrick; Beltran, Alejandra Gonzalez; Davies, Joel
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8161368

Introduction to deep learning

Autores: Anup Kumar, Alireza Khanteymoori
Publicado en: 2025
Editor: Galaxy Training Materials

Community onboarding cookbook published

Autores: Nikolay, Vazov
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.15826940

Onedata user-owned storage

Autores: Łukasz Opioła, Bartosz Walkowicz
Publicado en: 2025
Editor: Galaxy Training Materials

Comparison of two annotation tools - Helixer and Braker3

Autores: Romane LIBOUBAN
Publicado en: 2025
Editor: Galaxy Training Materials

Functional annotation of protein sequences

Autores: Anthony Bretaudeau
Publicado en: 2022
Editor: Galaxy Training Materials

Creating lightweight FAIR Digital Objects with RO-Crate and FAIR Signposting

Autores: Soiland-Reyes, Stian; Sefton, Peter; Castro, Leyla Jael; Coppens, Frederik; Garijo, Daniel; Leo, Simone; Portier, Marc; Groth, Paul; Goble, Carole
Publicado en: 2022
Editor: Zenodo
DOI: 10.5281/ZENODO.7245315

Genome annotation with Helixer

Autores: Romane LIBOUBAN, Anthony Bretaudeau
Publicado en: 2025
Editor: Galaxy Training Materials

FAIR-IMPACT synergies with EOSC4Cancer

Autores: Stian Soiland-Reyes; Carole Goble; Raquel Villodres Toledo; Romina Royo; Salvador Capella-Gutierrez
Publicado en: 2022
Editor: Zenodo
DOI: 10.5281/zenodo.6767548

EuroScienceGateway: WP2 introduction

Autores: Stian Soiland-Reyes; Carole Goble
Publicado en: EOSC, 2022
Editor: EOSC
DOI: 10.5281/zenodo.7152762

Exporting to Onedata remote

Autores: Łukasz Opioła, Bartosz Walkowicz
Publicado en: 2025
Editor: Galaxy Training Materials

Publication on the smart job scheduler implementation

Autores: Azab, Abdulrahman; Srikakulam, Sanjay Kumar; De Geest, Paul; Vondrák, Tomáš; Grüning, Björn; Kuntz, Mira; Fernandez-del-Castillo, Enol; Luna-Valero, Sebastian
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.15827107

Improving Galaxy provenance export using RO-Crate

Autores: De Geest, Paul; Coppens, Frederik; Eguinoa, Ignacio; Soiland-Reyes, Stian; Leo, Simone
Publicado en: 2022
Editor: Zenodo
DOI: 10.5281/ZENODO.7257145

Automating Galaxy workflows using the command line

Autores: Simon Bray, Wolfgang Maier
Publicado en: 2025
Editor: Galaxy Training Materials

EuroScienceGateway D2.1: Reproducible FAIR Digital Objects for Workflows

Autores: Soiland-Reyes, Stian; Chadwick, Eli; Bacall, Finn; Fernández, José M.; Grüning, Björn; Bayındır, Hakan
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.13225792

Analyse Argo data

Autores: Marie Josse
Publicado en: 2025
Editor: Galaxy Training Materials

Single-cell ATAC-seq standard processing with SnapATAC2

Autores: Timon Schlegel
Publicado en: 2025
Editor: Galaxy Training Materials

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

Autores: Łukasz Opioła, Bartosz Walkowicz
Publicado en: 2025
Editor: Galaxy Training Materials

Make your tools available on your subdomain

Autores: Marie Josse
Publicado en: 2024
Editor: Galaxy Training Materials

From NDVI data with OpenEO to time series visualisation with Holoviews

Autores: Marie Josse
Publicado en: 2024
Editor: Galaxy Training Materials

Use Apptainer containers for running Galaxy jobs

Autores: Torfinn Nome, Marius van den Beek, Matthias Bernt, Helena Rasche, Mira Kuntz
Publicado en: 2025
Editor: Galaxy Training Materials

Importing (uploading) data from Onedata

Autores: Łukasz Opioła, Bartosz Walkowicz
Publicado en: 2025
Editor: Galaxy Training Materials

Galaxy Installation with Ansible

Autores: Helena Rasche, Nate Coraor, Simon Gladman
Publicado en: 2019
Editor: Galaxy Training Materials

Create a subdomain for your community on UseGalaxy.eu

Autores: Marie Josse
Publicado en: 2024
Editor: Galaxy Training Materials

Bring Your Own Infrastructure

Autores: Pedersen, Maiken; Srikakulam, Sanjay Kumar; De Geest, Paul; Fernandez-del-Castillo, Enol; Cristofori, Andrea; Luna-Valero, Sebastian; Tangaro, Marco Antonio; Nicotri, Stefano
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.15729502

Customizing the look of Galaxy

Autores: Laila Los
Publicado en: 2023
Editor: Galaxy Training Materials

Marine Omics identifying biosynthetic gene clusters

Autores: Marie Josse
Publicado en: 2024
Editor: Galaxy Training Materials

Galaxy and Scientific Communities: How to Incorporate New Ones, Uplift Engaged Ones and Maintain Mature Ones

Autores: Liborio, L.; P. Austin; A. Gonzalez-Beltran; E. Chadwick; V. Savchenko; A. Neronov; J. Iaquinta; A. Bretaudeau
Publicado en: Conference: PASC2023 , Davos, Switzerland, 26-27 June 2023, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8114821

Masking repeats with RepeatMasker

Autores: Anthony Bretaudeau, Alexandre Cormier, Laura Leroi, Erwan Corre, Stéphanie Robin, Jonathan Kreplak
Publicado en: 2021
Editor: Galaxy Training Materials

Genome annotation with Helixer

Autores: Romane LIBOUBAN, Anthony Bretaudeau
Publicado en: 2025
Editor: Galaxy Training Materials

Best practices for workflows in GitHub repositories

Autores: Simone Leo, Eli Chadwick
Publicado en: 2023
Editor: Galaxy Training Materials

Interactive Tools (IT) in Galaxy

Autores: Kayikcioglu, Tunc; Srikakulam, Sanjay Kumar; Maier, Wolfgang; Grüning, Björn
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/ZENODO.8335099

Running Jobs on Remote Resources with Pulsar

Autores: Nate Coraor, Simon Gladman, Marius van den Beek, Helena Rasche, Gianmauro Cuccuru, Mira Kuntz
Publicado en: 2025
Editor: Galaxy Training Materials

Getting your hands-on earth data

Autores: Marie Josse
Publicado en: 2024, Página(s) GALAXY TRAINING
Editor: Galaxy Training Materials

Enabling an operational, open and FAIR EOSC ecosystem

Autores: Sebastian Schaaf,Anika Erxleben-Eggenhofer, Björn Grüning, The EuroScienceGateway Project
Publicado en: 2023
Editor: ELIXIR
DOI: 10.7490/F1000RESEARCH.1119627.1

RO-Crate - Introduction

Autores: Stian Soiland-Reyes, Peter Sefton
Publicado en: 2023
Editor: Galaxy Training Materials

Refining Genome Annotations with Apollo (eukaryotes)

Autores: Anthony Bretaudeau
Publicado en: 2025
Editor: Galaxy Training Materials

The Galaxy Platform and its Applications to Materials Science

Autores: Liborio, Leandro; Gonzalez-Beltran, Alejandra; Austin, Patrick; Chadwick, Eli
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8161429

Interactive Tools (IT) in Galaxy

Autores: Tunc Kayikcioglu University of Freiburg,Sanjay Kumar Srikakulam University of Freiburg, Wolfgang Maier University of Freiburg ,Björn Grüning University of Freiburg
Publicado en: 2023
Editor: TIB
DOI: 10.52825/CORDI.V1I.419

EuroScienceGateway Data Management Plan (DMP; D1.1)

Autores: Erxleben, Anika; Schaaf, Sebastian; D'Anna, Flora; Gruening, Bjoern; Coppens, Frederik
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/ZENODO.10054550

EuroscienceGateway Dissemination & Exploitation plan (D&E; D1.2)

Autores: Erxleben, Anika; Schaaf, Sebastian; Marchis, Oana; Gruening, Bjoern
Publicado en: 2023
Editor: 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

Autores: Iaquinta, Jean; Fouilloux, Anne
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.15600666

Galaxy Database schema

Autores: Hans-Rudolf Hotz, Björn Grüning
Publicado en: 2016
Editor: Galaxy Training Materials

Finding the muon stopping site with pymuon-suite in Galaxy

Autores: Leandro Liborio, Eli Chadwick, Patrick Austin
Publicado en: 2024
Editor: Galaxy Training Materials

Refining Genome Annotations with Apollo (prokaryotes)

Autores: Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet
Publicado en: 2021
Editor: Galaxy Training Materials

Getting started with Onedata distributed storage

Autores: Łukasz Opioła, Bartosz Walkowicz
Publicado en: 2025
Editor: Galaxy Training Materials

Creating high resolution images of Galaxy Workflows

Autores: Laila Los
Publicado en: 2024
Editor: Galaxy Training Materials

Ocean Data View (ODV)

Autores: Marie Josse
Publicado en: 2023
Editor: Galaxy Training Materials

EuroScienceGateway MS3: Initial EuroScienceGateway workflows registered

Autores: Soiland-Reyes, Stian; Grüning, Björn; De Geest, Paul
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.10728922

EuroScienceGateway D2.1: Reproducible FAIR Digital Objects for Workflows

Autores: Soiland-Reyes, Stian; Chadwick, Eli; Bacall, Finn; Fernández, José M.; Grüning, Björn; Bayındır, Hakan
Publicado en: 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
Editor: Zenodo
DOI: 10.5281/ZENODO.13225792

Genome Annotation

Autores: Anika Erxleben, Björn Grüning
Publicado en: 2015
Editor: Galaxy Training Materials

Ocean's variables study

Autores: Marie Josse
Publicado en: 2025
Editor: Galaxy Training Materials

Sentinel 5P data visualisation

Autores: Marie Josse
Publicado en: 2024
Editor: Galaxy Training Materials

Genome annotation with Funannotate

Autores: Anthony Bretaudeau
Publicado en: 2023
Editor: Galaxy Training Materials

D3.1 Operations documentation on the Open Infrastructure deployment

Autores: 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
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/ZENODO.15920451

Obis marine indicators

Autores: Marie Josse, Yvan Le Bras
Publicado en: 2023
Editor: Galaxy Training Materials

The Galaxy Platform: Applications to Catalysis Workflows

Autores: P. Austin; A. Gonzalez-Beltran; A. Nieva De La Hidalga; Liborio, L.
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8114859

Evaluating FAIR Digital Object and Linked Data as distributed object systems

Autores: Stian Soiland-Reyes, Carole Goble, Paul Groth
Publicado en: arXiv, 2023
Editor: CORNELL UNIVERSITY
DOI: 10.48550/arXiv.2306.07436

Conda, Container and Bots

Autores: Zierep, Paul; Srikakulam, Sanjay Kumar; Schaaf, Sebastian; Grüning, Björn
Publicado en: Proceedings of the Conference on Research Data Infrastructure, 2023, ISSN 2941-296X
Editor: 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

Autores: Marco Antonio Tangaro; Marica Antonacci; Giacinto Donvito; Nadina Foggetti; Pietro Mandreoli; Daniele Colombo; Graziano Pesole; Federico Zambelli
Publicado en: NAR Genomics and Bioinformatics, Edición 4, 2024, ISSN 2631-9268
Editor: Oxford University Press
DOI: 10.1093/NARGAB/LQAE140

RO-Crate: packaging metadata love notes into FAIR Digital Objects

Autores: Carole Goble, Stian Soiland-Reyes
Publicado en: Helmholtz Metadata Collaboration | Conference 2022, 2022
Editor: HMC
DOI: 10.5281/zenodo.7147703

Galaxy Training: A powerful framework for teaching!

Autores: 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
Publicado en: PLoS Computational Biology, Edición 1, 2023, ISSN 1544-9173
Editor: Public Library of Science
DOI: 10.1371/JOURNAL.PCBI.1010752

WorkflowHub: a registry for computational workflows

Autores: 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
Publicado en: Scientific Data, Edición 12, 2025, ISSN 2052-4463
Editor: Nature
DOI: 10.1038/S41597-025-04786-3

Integrative meta-omics in Galaxy and beyond

Autores: 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
Publicado en: Environmental Microbiome, 2023, ISSN 2524-6372
Editor: BMC
DOI: 10.1186/s40793-023-00514-9

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

Autores: 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
Publicado en: Genome Research, Edición 2, 2023, ISSN 1088-9051
Editor: 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

Autores: Abraham Nieva‐de‐la‐Hidalga, Leandro Liborio, Patrick Austin, Subindev Devadasan, Tom Underwood, Alexander Belozerov, Martin Wilding, Nitya Ramanan, C. Richard A. Catlow
Publicado en: ChemCatChem, Edición 17, 2025, ISSN 1867-3880
Editor: Wiley
DOI: 10.1002/CCTC.202401676

PLoS ONE

Autores: 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
Publicado en: PLOS ONE, 2024, ISSN 1932-6203
Editor: PLOS ONE
DOI: 10.48550/arxiv.2312.07852

Training Infrastructure as a Service

Autores: 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
Publicado en: Gigascience, 2023, ISSN 2047-217X
Editor: Oxford University Press
DOI: 10.1093/gigascience/giad048

Establishing the ELIXIR Microbiome Community

Autores: 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
Publicado en: F1000Research, Edición 13, 2024, ISSN 2046-1402
Editor: F1000 Research Ltd
DOI: 10.12688/F1000RESEARCH.144515.1

Finding workflows in the Galaxy universe: integrating a global ecosystem using workflow registries

Autores: 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
Publicado en: GALAXY AUSTRALIA, 2023
Editor: GALAXY AUSTRALIA
DOI: 10.5281/zenodo.8157531

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

Autores: 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
Publicado en: Microbial Genomics, Edición 10, 2024, ISSN 2057-5858
Editor: Microbiology Society
DOI: 10.1099/MGEN.0.001188

An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy

Autores: Anup Kumar, Gianmauro Cuccuru, Björn Grüning, Rolf Backofen
Publicado en: Gigascience, 2023, ISSN 2047-217X
Editor: Oxford University Press
DOI: 10.1093/gigascience/giad028

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

Autores: 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
Publicado en: Nature Biotechnology, Edición 42, 2024, ISSN 1087-0156
Editor: Springer Science and Business Media LLC
DOI: 10.1038/S41587-023-02100-3

Der europäische Galaxy-Server demokratisiert die Analyse biowissenschaftlicher Daten

Autores: Erxleben-Eggenhofer, Anika
Publicado en: Laborjournal, 2023, ISSN 1612-8354
Editor: LJ-Verlag Herfort und Sailer
DOI: 10.3030/101057388

Evaluating FAIR Digital Object and Linked Data as distributed object systems

Autores: Stian Soiland-Reyes; Carole Goble; Paul Groth
Publicado en: PeerJ Computer Science, 2024, ISSN 2376-5992
Editor: PeerJ Inc.
DOI: 10.48550/arxiv.2306.07436

Making workflow provenance FAIR across workflow systems with Workflow Run RO-Crate

Autores: 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
Publicado en: F1000RESEARCH, 2023
Editor: F1000RESEARCH
DOI: 10.5281/zenodo.8004793

Hydrogen Radical Chemistry at High-Symmetry {2Fe2S} Centers Probed Using a Muonium Surrogate

Autores: Joseph A. Wright, Farhana Haque, Leandro Liborio, Stephen P. Cottrell
Publicado en: Inorganic Chemistry, Edición 64, 2025, ISSN 0020-1669
Editor: American Chemical Society (ACS)
DOI: 10.1021/ACS.INORGCHEM.4C05126

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

Autores: Volodymyr Savchenko
Publicado en: SKAO, 2023
Editor: SKAO

Applying the FAIR Principles to computational workflows

Autores: 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
Publicado en: Scientific Data, Edición 1, 2025, ISSN 2052-4463
Editor: Nature
DOI: 10.1038/S41597-025-04451-9

Inorganic Chemistry

Autores: Wright, Joseph A., Farhana Haque, Leandro Liborio, and Stephen P. Cottrell
Publicado en: Inorganic Chemistry, Edición 10, 2025, ISSN 0020-1669
Editor: American Chemical Society
DOI: 10.1021/ACS.INORGCHEM.4C05126

DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data

Autores: Johanna Galvis, Joris Guyon, Benjamin Dartigues, Helge Hecht, Björn Grüning, Florian Specque, Hayssam Soueidan, Slim Karkar, Thomas Daubon, Macha Nikolski
Publicado en: Bioinformatics, Edición 40, 2024, ISSN 1367-4811
Editor: Oxford University Press (OUP)
DOI: 10.1093/BIOINFORMATICS/BTAE282

Electronic structure calculations for muon spectroscopy<sup>*</sup>

Autores: 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
Publicado en: Electronic Structure, Edición 7, 2025, ISSN 2516-1075
Editor: IOP Publishing
DOI: 10.1088/2516-1075/ADCB7C

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Autores: 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
Publicado en: Nucleic Acids Research, 2024, ISSN 1362-4962
Editor: Oxford University Press
DOI: 10.1093/NAR/GKAE410

An Ecosystem of Services for FAIR Computational Workflows

Autores: 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,
Publicado en: Arxiv, Computer Science, Distributed, Parallel, and Cluster Computing, 2025, ISSN 2331-8422
Editor: ArXiv
DOI: 10.48550/ARXIV.2505.15988

Recording provenance of workflow runs with RO-Crate

Autores: 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
Publicado en: PLOS ONE, Edición 19, 2024, ISSN 1932-6203
Editor: Public Library of Science (PLoS)
DOI: 10.1371/JOURNAL.PONE.0309210

Making workflow provenance FAIR across workflow systems with Workflow Run RO-Crate

Autores: 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
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8004793

Galaxy France: an example of a national UseGalaxy server

Autores: Siguret, Clea, Thomas Chaussepied, Romane Libouban, Eva Mercier, Julien Seiler, Bérénice Batut, Gildas Le Corguillé, and Anthony Bretaudeau
Publicado en: 2024
Editor: Galaxy Community Conference
DOI: 10.7490/F1000RESEARCH.1119767.1

Computing Simulations for Large Scale Experiments: the Case of Muons

Autores: Leandro Liborio; Patrick Austin; Alejandra Gonzalez Beltran; Joel Davies
Publicado en: 2023

Misconceptions about Galaxy debunked by the (French) Galaxy Community

Autores: Romane Libouban, Eva Mercier, Thomas Chaussepied, Bérénice Batut, Anthony Bretaudeau, Gildas Le Corguillé
Publicado en: JOBIM 2024 - Journées Ouvertes Biologie Informatique Mathématiques, Jun 2024, TOULOUSE, France. pp.1-28., 2024
Editor: HAL

Galaxy and RDM

Autores: Sebastian Schaaf, Anika Erxleben-Eggenhofer, Bjoern Gruening
Publicado en: Vol. 1 (2023): 1st Conference on Research Data Infrastructure (CoRDI) - Connecting Communities, 2023
Editor: 1st Conference on Research Data Infrastructure
DOI: 10.52825/cordi.v1i.421

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

Autores: Gildas Le Corguillé, Anthony Bretaudeau, Björn Grüning, Wendi Bacon, Bérénice Batut
Publicado en: JOBIM 2025 - Journées Ouvertes en bioinformatique et de la biostatistique francophone, Jul 2025, Bordeaux, France., 2025
Editor: HAL

Dynamic meta-scheduling in Galaxy with TPV Broker for smarter workload distribution

Autores: Srikakulam, Sanjay Kumar; Azab, Abdulrahman; De Geest, Paul; Vondrák, Tomáš; Kuntz, Mira; Luna-Valero, Sebastian; Grüning, Björn
Publicado en: 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.16312226

Climate Modeling with Conda and Containers to Improve Computational Resource Usage while Achieving Native Performance and Reproducibility

Autores: Iaquinta, Jean; Fouilloux, Anne; Ragan-Kelley, Benjamin
Publicado en: Crossref, 2025
Editor: Zenodo
DOI: 10.5281/ZENODO.15600119

Practical webby FDOs With RO-Crate and FAIR Signposting

Autores: Stian Soiland-Reyes; Peter Sefton; Simone Leo; Leyla Jael Castro; Claus Weiland; Herbert Van de Sompel
Publicado en: 2025
Editor: 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

Autores: Jean Iaquinta, Anne Fouilloux, Benjamin Ragan-Kelley
Publicado en: 2025
Editor: Copernicus GmbH
DOI: 10.5194/EGUSPHERE-EGU25-2605

Galaxy and Scientific Communities: How to Incorporate New Ones, Uplift Engaged Ones and Maintain Mature Ones

Autores: L. Liborio; P. Austin; A. Gonzalez-Beltran; E. Chadwick; V. Savchenko; A. Neronov; J. Iaquinta; A. Bretaudeau
Publicado en: PASC DAVOS, 2023
Editor: PASC DAVOS
DOI: 10.5281/zenodo.8114821

MuonGalaxy - tools, workflows and more for muons and materials science

Autores: Austin, Patrick; Davies, Joel; Gonzalez-Beltran, Alejandra; Liborio, Leandro
Publicado en: GALAXY PROJECT, 2023
Editor: GALAXY PROJEC
DOI: 10.5281/zenodo.8116071

Making EOSC Research Objects FAIR with RO-Crate: A common metadata overlay for EOSC repositories

Autores: Justin Clark-Casey; Stian Soiland-Reyes
Publicado en: EOSC, 2022
Editor: EOSC
DOI: 10.5281/zenodo.7323480

Implementation of a reproducible pipeline for producing seasonal Arctic sea ice forecasts

Autores: Vanessa Stöckl, Björn Grüning, Anne Fouilloux, Jean Iaquinta, Alejandro Coca-Castro
Publicado en: 2024
Editor: Copernicus GmbH
DOI: 10.5194/EGUSPHERE-EGU24-8343

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

Autores: Eva Mercier, Romane Libouban, Thomas Chaussepied, Anthony Bretaudeau
Publicado en: Application to Genome Annotation. JOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. 2024., 2024
Editor: HAL Open Science

Improving Galaxy provenance export using RO-Crate

Autores: Paul De Geest; Frederik Coppens; Ignacio Eguinoa; Stian Soiland-Reyes; Simone Leo
Publicado en: Research Ideas and Outcomes, 2022
Editor: MANCHESTER 1824
DOI: 10.5281/zenodo.7257146

The Galaxy Platform and its Applications to Materials Science

Autores: Leandro Liborio; Alejandra Gonzalez-Beltran; Patrick Austin; Eli Chadwick
Publicado en: STFC, 2024
Editor: GALAXY COMMUNITY HUB
DOI: 10.5281/zenodo.8161429

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

Autores: Jean Iaquinta, Anne Fouilloux
Publicado en: EGU General Assembly 2023, 2023
Editor: EGU General Assembly 2023
DOI: 10.5194/EGUSPHERE-EGU23-2579

Enhancing RDM in Galaxy by integrating RO-Crate

Autores: Paul De Geest; Frederik Coppens; Stian Soiland-Reyes; Ignacio Eguinoa; Simone Leo
Publicado en: Research Ideas and Outcomes, 2022
Editor: Research Ideas and Outcomes
DOI: 10.3897/rio.8.e95164

Improving Galaxy provenance export using RO-Crate

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

Making EOSC Research Objects FAIR with RO-Crate: A common metadata overlay for EOSC repositories

Autores: Clark-Casey, Justin; Soiland-Reyes, Stian
Publicado en: EOSC Symposium 2022 , Prague, CZ, 2022-11-14/--17 (Session FAIR enabling practices, Part A), 2022
Editor: Zenodo
DOI: 10.5281/zenodo.7323301

Unlocking the Potential of Containers in Scientific Computing to Achieve Bitwise Reproducibility, Portability and Performance

Autores: Jean Iaquinta, Anne Fouilloux
Publicado en: Communications in Computer and Information Science, Nordic e-Infrastructure Tomorrow, 2024, ISSN 1865-0937
Editor: Springer Nature Switzerland
DOI: 10.1007/978-3-031-86240-3_4

Integration of Nordugrid ARC with Galaxy and EGI IM

Autores: Maiken Pedersen, Balazs Konya, Sebastian Luna-Valero, Björn Grüning
Publicado en: Communications in Computer and Information Science, Nordic e-Infrastructure Tomorrow, 2025
Editor: Springer Nature Switzerland
DOI: 10.1007/978-3-031-86240-3_5

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