Orchestrating a community-developed computational workshop and accompanying training materials [version 1; referees: 2 approved]
Sean Davis,
Marcel Ramos,
Lori Shepherd,
Nitesh Turaga,
Ludwig Geistlinger,
Martin T. Morgan,
Benjamin Haibe-Kains,
Levi Waldron
Affiliations
Sean Davis
Center for Cancer Research, National Cancer Institute, USA, Bethesda, MD, 20892, USA
Marcel Ramos
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
Lori Shepherd
Roswell Park Cancer Institute, Buffalo, NY, 14203, USA
Nitesh Turaga
Roswell Park Cancer Institute, Buffalo, NY, 14203, USA
Ludwig Geistlinger
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
Martin T. Morgan
Roswell Park Cancer Institute, Buffalo, NY, 14203, USA
Benjamin Haibe-Kains
Princess Margaret Cancer Centre, University Health Network, Canada, Toronto, Ontario, M5G1L7, Canada
Levi Waldron
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
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.
