‘R’-eaching for the sky: facilitating R training in the Cloud

Biologists need data analysis skills to be able to interpret, visualise and communicate their research. R and RStudio are popular tools for robust and flexible data analysis but getting started with R can be daunting. While many generic R courses are available there is high demand for contextualised training in R for life scientists.

The Australian BioCommons and the National Bioinformatics Training Cooperative recently teamed up with Dr Saskia Freytag (Laboratory Head, Personalised Oncology Division, WEHI) to deliver a workshop on R: fundamental skills for biologists to a national audience. Saskia is passionate about empowering life scientists to use R and fostering connections with the R community. We’ve previously worked with Saskia to deliver a popular webinar on Getting Started with R. This workshop was based on a lesson on data analysis with R and Bioconductor that Saskia co-wrote as part of The Carpentries Incubator project. 

Over four, three hour sessions in June, 110 bioscientists from across Australia joined BioCommons online to start their journey in R. Participants came from both regional and metropolitan organisations, where they work on a variety of topics from conservation of native flora to infectious diseases. Lead trainers Saskia, Ms Adele Baraguhare (Monash Bioinformatics Platform), Dr Brendan Ansell (WEHI) and Dr Maria Doyle (Peter MacCallum Cancer Centre) guided participants through topics ranging from foundations and best practices to data analysis and visualisation and generating reports with packages such as ggplot2, dplyr, tidyverse and SummarizedExperiment. 

Importantly, participants also got the chance to put their new skills into action by working through hands-on exercises in small groups with support from a team of 23 facilitators. The workshop has already had an immediate positive impact on participants’ research.

“What would have taken me a long time to figure out before the workshop was comparably easy when I had to analyse my data today. The timing couldn't have been better to immediately apply the new skills!”

Participant: Julia Voelker, PhD Candidate, Southern Cross University.

The success of the workshop is down to the collaborative approach fostered by the National Bioinformatics Training Cooperative. By pooling resources and expertise we’re able to bring large groups of just the right people together - training more people more quickly and efficiently than any of us would be able to do alone. This model brings added benefits to the training community by fostering connections between trainers and the sharing of training best practice.

“The organisation was absolutely superb, one of the best I've ever seen, everything ran smoothly, adjusting as needed to keep to schedule. 

The other trainers were super to watch and learn from and the facilitators were also great to learn from through their answers in Slack.”

Lead trainer: Maria Doyle, Peter MacCallum Cancer Centre

Robust technical infrastructure was also key to the success and smooth running of this workshop. Through our connections with ARDC we were able to provide access to RStudio running on the ARDC Nectar Cloud avoiding the challenges of installing R across multiple systems. The BioCommons team setup identical machines for each of the trainers, facilitators and participants by using Nectar’s OpenStack API to create 150 copies of a machine with 2 cores and 4GB of RAM on which all packages and data were preinstalled and comprehensively tested by the trainers. This ensured a consistent and proven experience for all involved and meant that the workshop could spend more time focusing on the how and why of using R.

R is a fundamental skill for life scientists. To embark on your own R learning journey you can watch our webinar on Getting Started with R and access the training materials from this workshop via Zenodo. You can find out more about our training events like our upcoming workshop on Single Cell RNAseq analysis in R by following us on Twitter and LinkedIn or subscribing to our newsletter.