Minutes 2023-09-01

Author

Joseph Rickert

Published

September 1, 2023

  • Eric Nantz (Eli Lilly)
  • Heidi Curinckx (Johnson & Johnson)
  • HyeSoo Cho (FDA)
  • Jizu Zhi (FDA)
  • Joel Laxamana (Roche/Genentech)
  • Joseph Rickert (R Consortium)
  • Nan Xiao (Merck)
  • Ning Leng (Roche/Genentech)
  • Paul Schuette (FDA)
  • Robert Devine (Johnson & Johnson)
  • Saghir Bashir (Argenx)
  • Sam Parmar (Pfizer)

The meeting was recorded and the video is available.

Pilot 2

Paul Schuette provided and update on the Agency’s review of Pilot 2

  • HyeSoo Cho completed her review and passed it on to FDA authorities for additional review.
  • Paul feels that he and HyeSoo anticipate they will be able to answer any questions from the reviewers
  • Paul does not anticipate problems
  • It may take two weeks or longer to close things out
  • Paul will include some material about Pilot 1 in his up coming ASA data set

Actions:

  • Joel will send Paul the data set link used for Pilot 1
  • Joel will review the draft announcement for Pilot 3, Ning will approve and pass it to Paul for his review.

Pilot 3

Joel Laxamana provided the status update.

  • Did not use pkglite
  • submitted the .r file
  • Installed proprietary package from its own repo
  • Had to change .lock file to renv-lock.txt and provide instructions how to change it back.
  • Team members tested on Linux, Mac, and Windows
  • Submitted the Pilot through the FDA gateway
  • HyeSoo Cho, the FDA Pilot 3 reviewer, contacted the FDA gateway team to request access and expects to receive access next week
  • HyeSoo believes she will be able to report on Pilot 3 by the October meeting.

Pilot 4

Eric Nantz provided a status up date on Pilot 4 describing the significant progress that has been made with developing prototypes for both the WebAssemply and Container approaches.

WebAssembly

  • At 19:48 minutes in to the video Eric displays the Pilot 4 teams minutes for their recent meeting, Minutes 2023-08-18, and talks through the activities.
  • George Stagg and Winston Chang from Posit attended the Pilot 4 meeting
  • The httpuv R package will be necessary to start up a mini web server in the user’s local environment. There will be a script to accomplish this.
  • There will be no traces of the Shiny app interacting with the host system
  • Binaries of the packages used will be included in the transfer. These will not be executable binaries. They will be similar to .tar or .zip files.
  • The end user will have to install the version of R used in Pilot 1
  • Shinylive is another rapidly developing technology that may per pertinent to Pilot 4. Currently Shinylive is only available for Python. However, Winston Chang expects the R based version will be available soon.
  • Eric demos Shinylive from the posit website at 28:00 minutes into the video
  • See the Posit post webR 0.2.0 for additional information.
  • A Pilot 4 submission based on WebAssembly technology looks feasible by the end of the year.

Containers

  • Eric’s team already has a Podman container with Pilot 2 running
  • The team is waiting for Paul to clarify what is required by the FDA IT team for them be able to receive containers.

Preferred technology

  • Since the WebAssembly version does not require the involvement of FDA technology, it looks like it is the preferred method for a first Pilot 4 submission
  • At 37:43 minutes into the video, Eric shows the “Hello World” version of a WebAssembly submission created by Appsilon engineers.

Promotion

  • Joseph Rickert suggests that the story of the Submissions group cooperative effort is as important as the story of the technology.
  • The story of the overall submission group should be written up, However, Joe proposed that since the Pilot 4 effort is moving so quickly and involves contributions not only from working group members, but also from vendors we should tell this story first while the details are fresh.
  • Eric agrees that the participation of the two development teams from Posit and Appsilon is unique.
  • Eric notes that he has submitted a talk about Pilot 4 for the R/Pharma conference

Action:

  • Eric and Ning will update the GitHub sites for the Pilot teams to make sure the information is up to date and all the contributors are recognized.
  • Eric, Joe, Eric agree to work on an end of year thank you / celebration post.
  • Joe will make sure the R Consortium promotes Eric’s talk

Novo Nordisk Submission

  • Joe asked the group if anyone has information about the Novo Nordisk all R submission.
  • See the upcoming webinar

The next meeting of the working group will be at 9AM PST on Friday October 6, 2023.