Evidence map›Paper›PMID 36622853›Full record

ArticlePLoS computational biology2023

Galaxy Training: A powerful framework for teaching!

Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel Blankenberg, Pratik D Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué and 24 more

Abstract read
In one paragraph

Article in PLoS computational biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
63citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

63 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  7. Confrontations betweenApplied and environmental microbiology · 2026
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3 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

34 authors.

Saskia HiltemannClinical Bioinformatics Group, Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands.
Helena RascheClinical Bioinformatics Group, Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands.
Simon GladmanMelbourne Bioinformatics, University of Melbourne, Parkville, Victoria, Australia.
Hans-Rudolf HotzFriedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
Delphine LarivièreEberly College of Science, Pennsylvania State University, State College, Pennsylvania, United States of America.
Daniel BlankenbergGenomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America.ORCID 0000-0002-6833-9049
Pratik D JagtapDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America.
Thomas WollmannBiomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Heidelberg, Germany.
Anthony BretaudeauIGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France.
Nadia GouéAuBi, Mesocenter, Clermont Auvergne University, Aubière, France.
Timothy J GriffinDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America.
Coline RoyauxPNDB French Biodiversity e-infrastructure, PatriNat, French Museum of Natural History, Concarneau, France.
Yvan Le BrasPNDB French Biodiversity e-infrastructure, PatriNat, French Museum of Natural History, Concarneau, France.
Subina MehtaDepartment of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America.
Anna SymeMelbourne Bioinformatics, University of Melbourne, Parkville, Victoria, Australia.
Frederik CoppensDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
Bert DroesbekeDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
Nicola SoranzoEarlham Institute, Norwich Research Park, Norwich, United Kingdom.
Wendi BaconSchool of Life, Health and Chemical Sciences, The Open University, Milton Keynes, United Kingdom.
Fotis PsomopoulosInstitute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.
Cristóbal Gallardo-AlbaBioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
John DavisDepartment of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America.ORCID 0000-0002-1363-1245
Melanie Christine FöllInstitute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany.ORCID 0000-0002-1887-7543
Matthias FahrnerInstitute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany.
Maria A DoylePeter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
Beatriz Serrano-SolanoBioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
Anne Claire FouillouxSimula Research Laboratory, Oslo, Norway.
Peter van HeusdenSouth African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.ORCID 0000-0001-6553-5274
Wolfgang MaierBioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.ORCID 0000-0002-9464-6640
Dave ClementsAnaconda Inc, Austin, Texas, United States of America.ORCID 0000-0002-9970-6657
Florian HeylBioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
Galaxy Training Network
Björn GrüningBioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
Bérénice BatutBioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.ORCID 0000-0001-9852-1987

Funding

Implementing the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)U24HG010263 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI Enis Afgan, VINCENT JAMES CAREY · 2018 to 2026
$23.8M
Democratization of Data Analysis in Life Sciences Through GalaxyU24HG006620 · NHGRI · PENNSYLVANIA STATE UNIVERSITY, THE · PI Daniel James Blankenberg, Jeremy Goecks · 2021 to 2026
$9.8M
Turning big data analysis infrastructure for HIV researchR01AI134384 · NIAID · PENNSYLVANIA STATE UNIVERSITY, THE · PI NEKRUTENKO, ANTON, POND, SERGEI L KOSAKOVSKY · 2017 to 2021
$4.2M
A Federated Galaxy for user-friendly large-scale cancer genomics researchU24CA231877 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI GOECKS, JEREMY, SCHATZ, MICHAEL · 2018 to 2022
$3.9M
Expanding multiplexed kinase biosensor analysis to SWATH-MS (Part 2 of 2)U24CA199347 · NCI · UNIVERSITY OF MINNESOTA · PI GRIFFIN, TIMOTHY J. · 2016 to 2019
$2.4M
Biotechnology and Biological Sciences Research Council BB/CCG1720/1Medical Research Council MR/S035931/1NCI NIH HHS U24 CA199347NCI NIH HHS U24 CA231877NHGRI NIH HHS U24 HG006620NHGRI NIH HHS U24 HG010263NIAID NIH HHS R01 AI134384
6 · The paper itself

Abstract

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.

Indexed as

Computational BiologySoftwareData AnalysisHumansResearch Personnel

Identifiers

PMID36622853
PMCPMC9829167

What OpenQuestion holds

Textmetadata
LicenceCC0
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.