Testing Containers and WebAssembly in Submissions to the FDA
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The R Consortium Submission Working Group has now successfully made two pilot submissions to the FDA. All the submissions done by the group are focused on improving practices for R-based clinical trial regulatory submissions. Now, the R submission Working Groups, in collaboration with Appsilon and Posit, are exploring new technologies such as Containers and WebAssembly. In this article, we dive into the details of this exploration.
Table of Contents
- How Everything Started
- What’s next?
- The Journey with WebAssembly and Containers
- The Pilot 4 Shiny App Up and Running on webR!
- webR Shiny App
- Next Steps
How Everything Started
Pilot 1
This pilot was initially submitted on November 22, 2021. This submission was the first publicly available R-based submission to the FDA. This was a test submission that aimed to explore the submission of an R package to the FDA following the eCTD specifications. The submission included an R package, R scripts for analysis, R-based analysis data reviewed guide (ADRG), and other important components. The final response letter from the FDA was received on March 14, 2022.
Pilot 2
This was one of the first submission packages containing a Shiny application. The main goal of this pilot was to test the submission of an R-based Shiny application bundled into a submission package and transfer it successfully to FDA reviewers. The submitted application was built using the datasets and analyses that were used for the R Submission Pilot 1. The deployed version of this application is available on this site. Alternatively, a Rhino-based version of the application can be found here.
The final response letter from the FDA was reviewed on September 27, 2023.
What’s next?
Pilot 3
This pilot was successfully submitted to the FDA on Aug 28, 2023. This was the first publicly available R submission that included R scripts to produce ADaM datasets and TLFs. Both the ADaMs (SDTM .xpt sources from the CDISC Pilot study) and the TLFs (ADaMs .xpt sourced from the ADaMs generated in R by the Pilot 3 team) were created using R. The next step for this pilot is to await FDA’s review and approval, which may take several months to complete.
Pilot 4
This pilot aims to explore using technologies such as containers and WebAssembly software to package a Shiny application into a self-contained unit, streamlining the transfer and execution process for enhanced efficiency.
This pilot is expected to be divided into two parallel submissions:
(a) will investigate WebAssembly and
(b) will investigate containers.
The Journey with WebAssembly and Containers
Our team at Appsilon teamed up with the dynamic Pilot 4 crew to explore WebAssembly technology and containers. George Stagg and Winston Chang also joined the working group to discuss the web-assembly portion of Pilot 4. This partnership brought together our engineering prowess to contribute to these tools, injecting fresh perspectives into the ongoing pilot project.
Some of the outcomes of the collaboration:
- We were able to set up a robust container environment for this pilot project.
- We aided the progress made on the use of both experimental technologies: containers and WebAssembly.
- We developed a working prototype submission using Podman container technology.
- We developed a working early-stage prototype for wrapping a small Shiny application using WebAssembly.
WebAssembly
webr
WebAssembly allows languages like R to be executed at near-native speed directly within web browsers, providing users with the ability to run R code without having R installed locally. WebR is essentially the R programming language adapted to run in a web browser environment using WebAssembly. This project is under active development.
The Pilot 4 Shiny App Up and Running on webR!
The deployed example of the Shiny app running on webR is available here. Check out the video of the application running below.
Below is the dockerfile (recipe) for the container:
Next Steps
The next steps are waiting for the review of Pilot 3 by the FDA and to submit the two sections that explore the new technologies to regulatory authorities. Thanks to the collaboration between the R Submission Working Group and other institutions, there is already a working prototype of a {teal}-like Shiny application running on webR and further exploration with Podman is underway.
- Submission to FDA
- Rhino Compatibility
Appsilon is working on the side with Rhino compatibility; eventually, we might be able to just add this framework into the Pilot 4 application.
- {teal}This and other packages might be on CRAN soon. We could incorporate them after that, replacing the shims created for this version.
- Boot TimeWe need to improve boot time (remove dependencies and keep working on webR).
This article was co-authored by Pedro Silva, André Veríssimo, Vedha Viyash & Tymoteusz Makowski
This post was originally published on https://pharmaverse.github.io/.
The post appeared first on appsilon.com/blog/.
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