Encouraging computational reproducibility in research, we will present a variety of data stewardship recommendations that we have found useful in the process of training development. As part of that process, we are exploring the application of the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines to the Galaxy Training Network (GTN) materials, in order to improve their secondary use and adaptation.

This tutorial outlines how to set and use existing resources to make Galaxy training development and content creation FAIR.

Agenda

In this tutorial, we will cover:

1. Plan to share your training materials
2. Improve findability of your training materials by properly describing them
3. Give your training materials a unique identity
4. Register your training materials online
5. Define access rules for your training materials
6. Use an interoperable format for your training materials
7. Make your training materials (re)usable for trainers
8. Make your training materials usable for trainees
9. Make your training materials contribution friendly
10. Keep your training materials up-to-date
11. Conclusion

Here, we refer to a set of good practices as described in “Ten simple rules for making training materials FAIR” Garcia et al. 2020.

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Image credit: Luc Wiegers and Celia van Gelder Wiegers and van Gelder 2019

Plan to share your training materials

The Galaxy Training Network (GTN) provides researchers with online training materials, connects them with local trainers, and helps promoting open data analysis practices worldwide. It provides a record of training content development and ensure materials curation via cross-domain repositories (i.g., GitHub, Zenodo). Keeping your materials in the right places from the beginning will make it possible for you to more effectively and widely distribute your work without any duplication in contribution. Instruction where to start creating a new tutorial can be found at GTN contributing tutorial.

Improve findability of your training materials by properly describing them

Describing your training materials with structured metadata is fundamental to making them FAIR resource. Creating metadata boost findability and preserve information and can be updated after publication. GTN tutorial require several mandatory metadata information such as learning objectives following Bloom’s taxonomy Chevron 2014, prerequisites, time estimate, or questions addressed by the tutorial. Content developers needs to know where to find all of the available metadata to reference it later. Schema.org is a collaborative project with a mission to create the addition of structured metadata to web pages. It describes data using shared vocabulary. It is in this spirit that the BioSchemas community initiative was created to extend the Schema.org standard to life-science resources with training content specification. GTN offers schemas command line tutorial where metadata can be added or updated. This reduces the complexity of keywords and set the scene for controlled vocabularies environment. This increases the effectiveness of metadata filtering, which decreases ambiguity and makes it easier to find and retrieve information.

Give your training materials a unique identity

To support teachers and trainers, the GTN tutorials rely on specific tags and identifiers. Adding persistent identifiers (PIDs) to training materials makes them easy to cite and aids citation counting in research metric systems McMurry et al. 2017. Providing PIDs ensure that tag/identifier will continue to work even if webpage location changes. Data used for tutorials are required to be stored at Zenodo and associated with Digital Object Identifiers (DOI).

Register your training materials online

Sharing and publishing with the GTN training helps minimize the amount of time and effort required for instructors to prepare for and run their training courses and workshops, by providing templates and a complete training infrastructure. Online registry makes your content more discoverable and accessible to wider community. GTN tutorials are automatically registered on TeSS (ELIXIR Training e-support system).

Define access rules for your training materials

The GTN materials are designed to be flexible in their use, open access and community-driven. It is important to follow the hosting website disclaimers and keep materials metadata in place.

Use an interoperable format for your training materials

GTN Tutorials aim to follow best practices in course design, so that they can be used in different environments. Content of the tutorials and slides are written in Markdown and supported by templates. Metadata are stored in YAML and workflows in JSON. Self-contained structure allow others to tune or reuse existing content.

Make your training materials (re)usable for trainers

To help others determine whether the training materials are relevant and adaptable to their particular situations, metadata published alongside training materials should include context and sufficient description including: contributor details, license, description, learning outcomes, audience, requirements, tags/keywords, duration and last revision date Applying the proper licence and tagging training materials with metadata can make it simpler for others to (re)use and adapt them.

GTN provide strong technical support and set of contributing self learning material.

Make your training materials usable for trainees

Prerequisites and learning outcomes are particularly helpful metadata. To be effective, learning objectives must be written using active verbs that describe the expected trainee behaviours as well as the knowledge, skills, and expertise they will have received. Rich metadata requirements and SMART—Specific (Measurable, Attainable, Relevant, and Time-bound) learning outcomes following Bloom’s taxonomy Chevron 2014 helps to clarify which trainees will benefit most from the training. Self-learning structure of the GTN materials supported by slides and video walkthroughs/tours adds another layer of usability.

Make your training materials contribution friendly

GTN have clear guidelines for contribution and involvement. Community supported CONTRIBUTING files and chat offer the chance to exchange information such as contact details, expectations for contributions, and more. All contributors should be listed and thanked in the acknowledgements; how to cite the tutorial and give credit to contributors can be found at the end of each tutorial.

Keep your training materials up-to-date

It is crucial to keep your training materials up-to-date and so you are aware of any new features, trends, or improvements in the topic (such as updated tools or databases). Transparent peer-review and curation process in collaborative and open set up ensure materials quality.

Conclusion

There are many ways to improve the training content. It is crucial that we work together to make training materials FAIR so that everyone can benefit from them. These simple suggestions are intended to encourage dialogue and cooperation among Galaxy training community and help bring the latest developments to users.

The Galaxy Training Network is an example of a robust, effective Community of Practice. For more information please look at this great article Hiltemann et al. 2023, the corresponding FAIR guidelines “How does the GTN ensure our training materials are FAIR?” and follow short introduction to FAIR data stewardship.

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Key points

• FAIR principles in Galaxy training development and content creation.

Frequently Asked Questions

References

1. How does the GTN ensure our training materials are FAIR? Accessed 2023-05-23. https://training.galaxyproject.org/training-material/faqs/gtn/fair_training.html
2. Chevron, M.-P., 2014 A metacognitive tool: Theoretical and operational analysis of skills exercised in structured concept maps. Perspectives in Science 2: 46–54. 10.1016/j.pisc.2014.07.001
3. McMurry, J. A., N. Juty, N. Blomberg, T. Burdett, T. Conlin et al., 2017 Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS biology 15: e2001414. 10.1371/journal.pbio.2001414
4. Wiegers, L., and C. W. G. van Gelder, 2019 Illustration for "Ten simple rules for making training materials FAIR". 10.5281/zenodo.3593258
5. Garcia, L., B. Batut, M. L. Burke, M. Kuzak, F. Psomopoulos et al., 2020 Ten simple rules for making training materials FAIR (S. Markel, Ed.). PLOS Computational Biology 16: e1007854. 10.1371/journal.pcbi.1007854
6. Hiltemann, S., H. Rasche, S. Gladman, H.-R. Hotz, D. Larivière et al., 2023 Galaxy Training: A powerful framework for teaching! PLOS Computational Biology 19: e1010752. 10.1371/journal.pcbi.1010752

Glossary

FAIR

Findable, Accessible, Interoperable, Reusable

GTN

Galaxy Training Network

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Citing this Tutorial

1. Katarzyna Kamieniecka, Krzysztof Poterlowicz, FAIR Galaxy Training Material (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/contributing/tutorials/fair-gtn/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{contributing-fair-gtn,
author = "Katarzyna Kamieniecka and Krzysztof Poterlowicz",
	title = "FAIR Galaxy Training Material (Galaxy Training Materials)",
	year = "",
	month = "",
	day = ""
	url = "\url{https://training.galaxyproject.org/training-material/topics/contributing/tutorials/fair-gtn/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol} Computational Biology}
}

                   

Funding

These individuals or organisations provided funding support for the development of this resource

DASH UK

This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.

Developing GTN training material

This tutorial is part of a series to develop GTN training material, feel free to also look at:

1. Contributing with GitHub via command-line
2. Overview of the Galaxy Training Material
3. Creating Interactive Galaxy Tours
4. Contributing with GitHub via its interface
5. Generating PDF artefacts of the website
6. Tools, Data, and Workflows for tutorials
7. Teaching Python
8. Running the GTN website online using GitHub CodeSpaces
9. Design and plan session, course, materials
10. GTN Metadata
11. Running the GTN website online using GitPod
12. Adding auto-generated video to your slides
13. Including a new topic
14. Adding Quizzes to your Tutorial
15. Principles of learning and how they apply to training and teaching
16. Updating diffs in admin training
17. Running the GTN website locally using the command line
18. Creating a new tutorial
19. Single Cell Publication - Data Plotting
20. FAIR Galaxy Training Material
21. Single Cell Publication - Data Analysis
22. Creating content in Markdown
23. Creating Slides

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/fair-gtn/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

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