Galaxy Training: A powerful framework for teaching!


Journal

PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922

Informations de publication

Date de publication:
01 2023
Historique:
entrez: 9 1 2023
pubmed: 10 1 2023
medline: 12 1 2023
Statut: epublish

Résumé

There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.

Identifiants

pubmed: 36622853
doi: 10.1371/journal.pcbi.1010752
pii: PCOMPBIOL-D-22-00888
pmc: PMC9829167
doi:

Types de publication

Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

e1010752

Subventions

Organisme : NCI NIH HHS
ID : U24 CA199347
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA231877
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG010263
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG006620
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI134384
Pays : United States
Organisme : Medical Research Council
ID : MR/S035931/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/CCG1720/1
Pays : United Kingdom

Informations de copyright

Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Déclaration de conflit d'intérêts

We have read the journal’s policy and the authors of this manuscript have the following competing interests: DB has a significant financial interest in GalaxyWorks, a company that may have a commercial interest in the results of this research and technology. This potential conflict of interest has been reviewed and is managed by the Cleveland Clinic. This does not alter our adherence to all the PLOS Computational Biology policies on sharing data and materials.

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Auteurs

Saskia Hiltemann (S)

Clinical Bioinformatics Group, Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands.

Helena Rasche (H)

Clinical Bioinformatics Group, Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands.
Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
Academie voor de Technologie van Gezondheid en Milieu, Avans Hogeschool, Breda, the Netherlands.

Simon Gladman (S)

Melbourne Bioinformatics, University of Melbourne, Parkville, Victoria, Australia.

Hans-Rudolf Hotz (HR)

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

Delphine Larivière (D)

Eberly College of Science, Pennsylvania State University, State College, Pennsylvania, United States of America.

Daniel Blankenberg (D)

Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America.

Pratik D Jagtap (PD)

Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America.

Thomas Wollmann (T)

Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Heidelberg, Germany.

Anthony Bretaudeau (A)

IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France.
GenOuest Core Facility, Univ Rennes, Inria, CNRS, IRISA, Rennes, France.

Nadia Goué (N)

AuBi, Mesocenter, Clermont Auvergne University, Aubière, France.

Timothy J Griffin (TJ)

Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America.

Coline Royaux (C)

PNDB French Biodiversity e-infrastructure, PatriNat, French Museum of Natural History, Concarneau, France.

Yvan Le Bras (Y)

PNDB French Biodiversity e-infrastructure, PatriNat, French Museum of Natural History, Concarneau, France.

Subina Mehta (S)

Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America.

Anna Syme (A)

Melbourne Bioinformatics, University of Melbourne, Parkville, Victoria, Australia.

Frederik Coppens (F)

Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
VIB Center for Plant Systems Biology, Ghent, Belgium.

Bert Droesbeke (B)

Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
VIB Center for Plant Systems Biology, Ghent, Belgium.

Nicola Soranzo (N)

Earlham Institute, Norwich Research Park, Norwich, United Kingdom.

Wendi Bacon (W)

School of Life, Health and Chemical Sciences, The Open University, Milton Keynes, United Kingdom.

Fotis Psomopoulos (F)

Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.

Cristóbal Gallardo-Alba (C)

Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.

John Davis (J)

Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America.

Melanie Christine Föll (MC)

Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany.
Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts, United States of America.
German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany.

Matthias Fahrner (M)

Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany.
German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany.

Maria A Doyle (MA)

Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.

Beatriz Serrano-Solano (B)

Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
ELIXIR Germany, Institute of Bio- and Geosciences (IBG-5)-Computational Metagenomics, Forschungszentrum Jülich GmbH, Jülich, Germany.
Euro-BioImaging ERIC Bio-Hub, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

Anne Claire Fouilloux (AC)

Simula Research Laboratory, Oslo, Norway.

Peter van Heusden (P)

South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.

Wolfgang Maier (W)

Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.

Dave Clements (D)

Anaconda Inc, Austin, Texas, United States of America.

Florian Heyl (F)

Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.

Björn Grüning (B)

Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.

Bérénice Batut (B)

Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.

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