Fostering Accessible Online Education Using Galaxy as an e-learning Platform

Serrano-Solano, Beatriz; Föll, Melanie Christine; Gallardo-Alba, Cristóbal; Erxleben, Anika; Rasche, Helena; Hiltemann, Saskia; Fahrner, Matthias; Dunning, Mark J.; Schulz, Marcel H.; Scholtz, Beáta; Clements, D. L.; Nekrutenko, Anton; Batut, Bérénice; Grüning, Björn

doi:10.20944/preprints202009.0457.v1

Cited by 7 publications

(11 citation statements)

References 13 publications

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“…Galaxy and the GTN cater to remote learners and teachers with a set of features to facilitate the online learning process. It provides easy access to data and the possibility to share the progress and achievements, both student-to-student and student-to-instructor [33]. This has been extensively tested during the COVID-19 pandemic.…”

Section: Training In the Covid-19 Era: Remote Learningmentioning

confidence: 99%

Galaxy Training: A Powerful Framework for Teaching!

Hiltemann

Rasche

Gladman

et al. 2022

Preprint

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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 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

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Section: Training In the Covid-19 Era: Remote Learningmentioning

confidence: 99%

Galaxy Training: A Powerful Framework for Teaching!

Hiltemann

Rasche

Gladman

et al. 2022

Preprint

Self Cite

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“…This platform, originally conceived as a research tool, integrates a community-driven teaching framework with a wide collection of training materials covering diverse bioinformatics domains [ 63 , 64 ]. Some practical recommendations for using Galaxy as an e-learning platform have been compiled in Serrano-Solano and colleagues [ 11 ].…”

Section: A Constructivist Approach To Bioinformatics Educationmentioning

confidence: 99%

“…Constructivism considers that the best way to acquire knowledge is through active experimentation in real contexts which encourage the selection, organization, and integration of their experiences with their previous knowledge in a social context [ 9 , 10 ]. Due to its social nature, the role of technology in constructivist online teaching practices should be the creation of learning environments focused on the collective construction of knowledge rather than simply a vehicle for the delivery of content [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

“…We propose different tools, such as GitHub and the Galaxy platform for bioinformatics data analysis, as example frameworks to make those recommendations more illustrative (see Box 1 for practical tips). It will also set the ground for trainers to organize their bioinformatics lessons by establishing the theoretical basis for our recommendations on online teaching described in Serrano-Solano and colleagues [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

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A constructivist-based proposal for bioinformatics teaching practices during lockdown

2021

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The Coronavirus Disease 2019 (COVID-19) outbreaks have caused universities all across the globe to close their campuses and forced them to initiate online teaching. This article reviews the pedagogical foundations for developing effective distance education practices, starting from the assumption that promoting autonomous thinking is an essential element to guarantee full citizenship in a democracy and for moral decision-making in situations of rapid change, which has become a pressing need in the context of a pandemic. In addition, the main obstacles related to this new context are identified, and solutions are proposed according to the existing bibliography in learning sciences.

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“…For the last decade, many HPC and Cloud-based NGS command-line programs or webbased platforms have wrapped popular high-level analysis and visualisation tools in an intuitive and appealing interface [15]. Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org, Australia: https://usegalaxy.org.au/) in particular has been successful in establishing itself as an analytics hub and an e-learning platform with global scientists, intending to produce accessible, reproducible and collaborative biological analyses [16,17].…”

Section: Introductionmentioning

confidence: 99%

easyfm: An easy software suite for file manipulation of Next Generation Sequencing data on desktops

Jung

Jeon

Ortiz‐Barrientos

2021

Preprint

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Storing and manipulating Next Generation Sequencing (NGS) file formats is an essential but difficult task in biological data analysis. The easyfm ( easy f ile m anipulation) toolkit ( https://github.com/TaekAndBrendan/easyfm ) makes manipulating commonly used NGS files more accessible to biologists. It enables them to perform end-to-end reproducible data analyses using a free standalone desktop application (available on Windows, Mac and Linux). Unlike existing tools (e.g. Galaxy), the Graphical User Interface (GUI)-based easyfm is not dependent on any high-performance computing (HPC) system and can be operated without an internet connection. This specific benefit allow easyfm to seamlessly integrate visual and interactive representations of NGS files, supporting a wider scope of bioinformatics applications in the life sciences.

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Fostering Accessible Online Education Using Galaxy as an e-learning Platform

Cited by 7 publications

References 13 publications

Galaxy Training: A Powerful Framework for Teaching!

Galaxy Training: A Powerful Framework for Teaching!

A constructivist-based proposal for bioinformatics teaching practices during lockdown

easyfm: An easy software suite for file manipulation of Next Generation Sequencing data on desktops

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