Janssen’s R Service for Visualization and Processing 2017-07-25T15:27:17+00:00

Janssen’s R Service for Visualization and Processing

Zach Schleien
ITLDP Analyst, Business Technology Leader at Johnson & Johnson

WAZE

Caring for the world, one person at a time, inspires and unites the people of Johnson & Johnson. The mission of the R&D Emerging Technologies Team, within the Janssen pharmaceutical companies of Johnson & Johnson, is to facilitate a paradigm shift for computational and data scientists, deploying scalable platform solutions with limitless computational power. By embracing innovation and improving collaboration they strive to enable the breakthroughs that help people everywhere live longer, healthier, happier lives.

Zach Schleien, ITLDP Analyst, Business Technology Leader

The Janssen Global Epidemiology department has built a tool using R and Shiny to conduct network meta-analyses using data from ClinicalTrials.gov.

The Challenge

Janssen scientists are most efficient when they have the ability to easily share code and applications, and collaborate with colleagues. They are looking to conduct their analyses in R, develop Shiny applications to share with other scientists and business colleagues across J&J, and submit R batch jobs to an HPC cluster. Traditional RStudio Server and Shiny environments employ single-node setups, with a shared drive between them to store R packages and host Shiny apps. However, the team determined that this setup would not scale well with increasing demands for compute or memory.

The Solution

The Emerging Technologies team specializes in High Performance Computing (HPC) and Elastic Cloud Computing. They developed RSVP: The R Service for Visualization and Processing. Explained simply, it’s R as a service. RSVP is a robust R/Shiny computing environment for scientists throughout Janssen.

Johnson & Johnson leverages Amazon Web Services (AWS) and has a designated virtual private cloud team (VPCx) on-site. The Emerging Technologies team built an environment as a cluster containing a master node, any number of personal nodes, and a burstable computing grid for on-demand “embarrassingly parallel” compute power. Shiny Server Pro and RStudio live on the master node. Once a user joins the environment and creates a folder to store their Shiny applications they then see an RStudio GUI and have the ability to run Shiny applications from their home folder.

Why RStudio?

RStudio Shiny Server Pro and RStudio Server provided the right tooling for scientists and complemented the team’s background in clusters and Chef, allowing them to scale and make enhancements to their environment as needed. When an enhancement needs to be made, it requires minimal work to a Chef cookbook.

Before, Janssen scientists often had to use a second computer to perform their R analysis, since their work consumed too much computational power for a single laptop. For example, it took one scientist 2.5 days to run his analysis conducting feature selection and permutation testing markers predicting Alzheimer’s disease risk. With RStudio and Shiny Server Pro in RSVP, the time to spin up RStudio and update his application has been reduced to a half-day!

The Payoff

A variety of teams from Johnson & Johnson are now using the RSVP service. Scientists from the Integrative Solutions team are building models to help predict the relapse of schizophrenia. The Janssen Global Epidemiology department has built a tool using R and Shiny to conduct network meta-analyses using data from ClinicalTrials.gov.

Too often, scientists are siloed based on organizational structures. Through RSVP and applications such as Slack, the Emerging Technologies team is enabling scientists within Janssen to share and collaborate with colleagues outside of their immediate networks. This has been instrumental in growing the Shiny community, but more importantly, it has allowed for the exchange of ideas. The team continues to work with RStudio to nurture more Shiny applications in drug development and combining Shiny and R Markdown for interactive & reproducible analysis.

By Zachary Schleien, Taylor Hamilton, Juan Carlos Coronel

About RStudio

RStudio provides open source and enterprise-ready professional software for the R community. We are inspired by the people who use our products to understand and improve the world through data analysis.