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F1000Res. 2018 Oct 17;7:1656. doi: 10.12688/f1000research.16516.1. eCollection 2018.

Orchestrating a community-developed computational workshop and accompanying training materials.

Author information

1
Center for Cancer Research, National Cancer Institute, USA, Bethesda, MD, 20892, USA.
2
Graduate School of Public Health and Health Policy and the Institute for Implementation Science in Population Health, City University of New York, New York, NY, 10027, USA.
3
Roswell Park Cancer Institute, Buffalo, NY, 14203, USA.
4
Princess Margaret Cancer Centre, University Health Network, Canada, Toronto, Ontario, M5G1L7, Canada.
5
Medical Physics Department, University of Toronto, Toronto, Ontario, M5G1L7, Canada.

Abstract

The importance of bioinformatics, computational biology, and data science in biomedical research continues to grow, driving a need for effective instruction and education. A workshop setting, with lectures and guided hands-on tutorials, is a common approach to teaching practical computational and analytical methods. Here, we detail the process we used to produce high-quality, community-authored educational materials that are available for public consumption and reuse. The coordinated efforts of 17 authors over 10 weeks resulted in 15 workshops available as a website and as a 388-page electronic book. We describe how we utilized cloud infrastructure, GitHub, and a literate programming approach to robustly deliver hands-on tutorials to participants of the annual Bioconductor conference. The scripts, raw and published workshop materials, and cloud machine image are all openly available. Our approach uses free services and software and can be adapted by workshop organizers and authors in other contests with appropriate technical backgrounds.

KEYWORDS:

Bioconductor; R; bioinformatics; education; github; informatics; literate programming; markdown; open source; software

PMID:
30473781
PMCID:
PMC6234736
DOI:
10.12688/f1000research.16516.1
[Indexed for MEDLINE]
Free PMC Article

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