Evidence map›Paper›PMID 37395629›Full record

ArticleGigaScience2022

Training Infrastructure as a Service.

Helena Rasche, Cameron Hyde, John Davis, Simon Gladman, Nate Coraor, Anthony Bretaudeau, Gianmauro Cuccuru, Wendi Bacon, Beatriz Serrano-Solano, Jennifer Hillman-Jackson and 4 more

Open access · goldAbstract read
In one paragraph

Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.4field-weighted citation impact, top 40% of its field
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

5 citing papers in PubMed, 7 citations in OpenAlex.

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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

14 authors at 9 institutions in 6 countries.

Helena RascheDepartment of Pathology and Clinical Bioinformatics, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands.ORCID 0000-0001-9760-8992
Cameron HydeQueensland Cyber Infrastructure Foundation Ltd., The University of Queensland, St. Lucia, QLD 4072, Australia.ORCID 0000-0002-5913-9766
John DavisDepartment of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0002-1363-1245
Simon GladmanMelbourne Bioinformatics, The University of Melbourne, Melbourne, VIC 3051, Australia.ORCID 0000-0002-6100-4385
Nate CoraorSchool of Life, Health & Chemical Sciences, The Open University, Milton Keynes MK7 6AA, UK.ORCID 0000-0001-8083-2963
Anthony BretaudeauIGEPP, INRAE, Institut Agro, University of Rennes, 35000 Rennes, France.ORCID 0000-0003-0914-2470
Gianmauro CuccuruBioinformatics Grou, Department of Computer Science, University of Freiburg, 79110 Freiburg im Breisgau, Germany.ORCID 0000-0002-5335-545X
Wendi BaconSchool of Life, Health & Chemical Sciences, The Open University, Milton Keynes MK7 6AA, UK.ORCID 0000-0002-8170-8806
Beatriz Serrano-SolanoEuro-Bioimaging ERIC Bio-Hub, EMBL, 69117 Heidelberg, Germany.ORCID 0000-0002-5862-6132
Jennifer Hillman-JacksonEuro-Bioimaging ERIC Bio-Hub, EMBL, 69117 Heidelberg, Germany.ORCID 0000-0003-4012-8116
Saskia HiltemannDepartment of Pathology and Clinical Bioinformatics, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands.ORCID 0000-0003-3803-468X
Miaomiao ZhouSchool of Life Sciences and Technology, Avans University of Applied Sciences, Lovensdijkstraat 63, 4818 AJ Breda, the Netherlands.ORCID 0000-0003-4426-1758
Björn GrüningBioinformatics Grou, Department of Computer Science, University of Freiburg, 79110 Freiburg im Breisgau, Germany.ORCID 0000-0002-3079-6586
Andrew StubbsDepartment of Pathology and Clinical Bioinformatics, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands.ORCID 0000-0001-9817-9982
Avans University of Applied Sciences · NLErasmus MC · NLEuropean Molecular Biology Organization · DEThe Open University · GBUniversity of Freiburg · DECentre National de la Recherche Scientifique · FRJohns Hopkins University · USThe University of Melbourne · AUThe University of Queensland · AU

Funding

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
NHGRI NIH HHS U24 HG006620
6 · The paper itself

Abstract

backgroundHands-on training, whether in bioinformatics or other domains, often requires significant technical resources and knowledge to set up and run. Instructors must have access to powerful compute infrastructure that can support resource-intensive jobs running efficiently. Often this is achieved using a private server where there is no contention for the queue. However, this places a significant prerequisite knowledge or labor barrier for instructors, who must spend time coordinating deployment and management of compute resources. Furthermore, with the increase of virtual and hybrid teaching, where learners are located in separate physical locations, it is difficult to track student progress as efficiently as during in-person courses.

findingsOriginally developed by Galaxy Europe and the Gallantries project, together with the Galaxy community, we have created Training Infrastructure-as-a-Service (TIaaS), aimed at providing user-friendly training infrastructure to the global training community. TIaaS provides dedicated training resources for Galaxy-based courses and events. Event organizers register their course, after which trainees are transparently placed in a private queue on the compute infrastructure, which ensures jobs complete quickly, even when the main queue is experiencing high wait times. A built-in dashboard allows instructors to monitor student progress.

conclusionsTIaaS provides a significant improvement for instructors and learners, as well as infrastructure administrators. The instructor dashboard makes remote events not only possible but also easy. Students experience continuity of learning, as all training happens on Galaxy, which they can continue to use after the event. In the past 60 months, 504 training events with over 24,000 learners have used this infrastructure for Galaxy training.

Indexed as

LearningSoftwareComputational BiologyEuropeHumansGalaxyremote trainingteachingtraining

Identifiers

PMID37395629
PMCPMC10316688
OpenAlexW4382919136

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.