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Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research

View ORCID ProfileZena Lapp, View ORCID ProfileKelly L. Sovacool, View ORCID ProfileNick Lesniak, View ORCID ProfileDana King, View ORCID ProfileCatherine Barnier, View ORCID ProfileMatthew Flickinger, View ORCID ProfileJule Krüger, View ORCID ProfileCourtney R. Armour, View ORCID ProfileMaya M. Lapp, View ORCID ProfileJason Tallant, View ORCID ProfileRucheng Diao, View ORCID ProfileMorgan Oneka, View ORCID ProfileSarah Tomkovich, View ORCID ProfileJacqueline Moltzau Anderson, View ORCID ProfileSarah K. Lucas, View ORCID ProfilePatrick D. Schloss
doi: https://doi.org/10.1101/2021.06.15.448091
Zena Lapp
1Department of Computational Medicine & Bioinformatics, University of Michigan
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Kelly L. Sovacool
1Department of Computational Medicine & Bioinformatics, University of Michigan
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Nick Lesniak
2Department of Microbiology & Immunology, University of Michigan
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Dana King
3BRCF Bioinformatics Core, University of Michigan
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Catherine Barnier
1Department of Computational Medicine & Bioinformatics, University of Michigan
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Matthew Flickinger
4Department of Biostatistics, University of Michigan
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Jule Krüger
5Center for Political Studies, Institute for Social Research, University of Michigan
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Courtney R. Armour
2Department of Microbiology & Immunology, University of Michigan
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Maya M. Lapp
6Independent educator
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Jason Tallant
7Biological Station, University of Michigan
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Rucheng Diao
1Department of Computational Medicine & Bioinformatics, University of Michigan
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Morgan Oneka
1Department of Computational Medicine & Bioinformatics, University of Michigan
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Sarah Tomkovich
2Department of Microbiology & Immunology, University of Michigan
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Jacqueline Moltzau Anderson
2Department of Microbiology & Immunology, University of Michigan
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Sarah K. Lucas
2Department of Microbiology & Immunology, University of Michigan
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Patrick D. Schloss
2Department of Microbiology & Immunology, University of Michigan
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  • For correspondence: pschloss@umich.edu
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Summary

Inspired by well-established material and pedagogy provided by The Carpentries (Wilson 2016), we developed a two-day workshop curriculum that teaches introductory R programming for managing, analyzing, plotting and reporting data using packages from the tidyverse (Wickham et al. 2019), the Unix shell, version control with git, and GitHub. While the official Software Carpentry curriculum is comprehensive, we found that it contains too much content for a two-day workshop. We also felt that the independent nature of the lessons left learners confused about how to integrate the newly acquired programming skills in their own work. Thus, we developed a new curriculum that aims to teach novices how to implement reproducible research principles in their own data analysis. The curriculum integrates live coding lessons with individual-level and group-based practice exercises, and also serves as a succinct resource that learners can reference both during and after the workshop. Moreover, it lowers the entry barrier for new instructors as they do not have to develop their own teaching materials or sift through extensive content. We developed this curriculum during a two-day sprint, successfully used it to host a two-day virtual workshop with almost 40 participants, and updated the material based on instructor and learner feedback. We hope that our new curriculum will prove useful to future instructors interested in teaching workshops with similar learning objectives.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/umcarpentries/intro-curriculum-r

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 16, 2021.
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Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research
Zena Lapp, Kelly L. Sovacool, Nick Lesniak, Dana King, Catherine Barnier, Matthew Flickinger, Jule Krüger, Courtney R. Armour, Maya M. Lapp, Jason Tallant, Rucheng Diao, Morgan Oneka, Sarah Tomkovich, Jacqueline Moltzau Anderson, Sarah K. Lucas, Patrick D. Schloss
bioRxiv 2021.06.15.448091; doi: https://doi.org/10.1101/2021.06.15.448091
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Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research
Zena Lapp, Kelly L. Sovacool, Nick Lesniak, Dana King, Catherine Barnier, Matthew Flickinger, Jule Krüger, Courtney R. Armour, Maya M. Lapp, Jason Tallant, Rucheng Diao, Morgan Oneka, Sarah Tomkovich, Jacqueline Moltzau Anderson, Sarah K. Lucas, Patrick D. Schloss
bioRxiv 2021.06.15.448091; doi: https://doi.org/10.1101/2021.06.15.448091

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