Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Updated the table for containers_and_webassembly_submissions.qmd #109

Merged
merged 1 commit into from
Feb 1, 2024
+23 −23
Merged

Updated the table for containers_and_webassembly_submissions.qmd #109

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
46 changes: 23 additions & 23 deletions ...s/2024-02-01_containers_webassembly_submission/containers_and_webassembly_submissions.qmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ long_slug <- "2023-12-30_containers_webassembly_submission"

<!--------------- post begins here ----------------->

[The R Consortium Submission Working Group](https://www.r-consortium.org/) 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](https://appsilon.com/) and Posit are exploring new technologies such as Containers and WebAssembly. In this article, we dive into the details of this exploration.
[The R Consortium Submission Working Group](https://www.r-consortium.org/) 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](https://appsilon.com/) and Posit, are exploring new technologies such as Containers and WebAssembly. In this article, we dive into the details of this exploration.

## How Everything Started

Expand All @@ -34,19 +34,19 @@ This pilot was initially submitted on November 22, 2021. **This submission was t

## 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](https://github.com/RConsortium/submissions-pilot2-to-fda) was built using the datasets and analysis that were used for the R Submission Pilot 1. The deployed version of this application is available on [this site](https://rconsortium.shinyapps.io/submissions-pilot2/). Alternatively, a Rhino-based version of the application can be found [here](https://connect.appsilon.com/rhino-fda-pilot/).
**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](https://github.com/RConsortium/submissions-pilot2-to-fda) 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](https://rconsortium.shinyapps.io/submissions-pilot2/). Alternatively, a Rhino-based version of the application can be found [here](https://connect.appsilon.com/rhino-fda-pilot/).

The final response letter from the FDA was reviewed on September 27, 2023.

![](images/teal.png){fig-align="center" width="159"}

In this submission, there were many open-source R packages that were used to create and execute the Shiny application. A very well known shiny-based interactive exploration framework **{teal}** was used mainly for analyzing the clinical trial data; this package is included in the pharmaverse package repository. The full list of open-source and proprietary R analysis packages is available on this [Analysis Data Reviewer's Guide](https://rsubmission-draft.website-us-east-1.linodeobjects.com/) prepared by the R Consortium R Submissions Working Group for the Pilot 2.
In this submission, there were many open-source R packages that were used to create and execute the Shiny application. A very well-known shiny-based interactive exploration framework **{teal}** was used mainly for analyzing the clinical trial data; this package is included in the pharmaverse package repository. The full list of open-source and proprietary R analysis packages is available on this [Analysis Data Reviewer's Guide](https://rsubmission-draft.website-us-east-1.linodeobjects.com/) prepared by the R Consortium R Submissions Working Group for the Pilot 2.

# What's next?

## Pilot 3

This pilot was successfully submitted to FDA on Aug 28, 2023. **This was the first publicly available R [submission](https://github.com/RConsortium/submissions-pilot3-adam-to-fda) 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 steps for this pilot is to await FDA's review and approval which may take several months to complete.
This pilot was successfully submitted to the FDA on Aug 28, 2023. **This was the first publicly available R [submission](https://github.com/RConsortium/submissions-pilot3-adam-to-fda) 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

Expand Down Expand Up @@ -94,7 +94,7 @@ During the **second iteration**, which was recently held, Pedro Silva shared the

#### The Process

1. **Leverage last 2 iterations of the application**
1. **Leverage the last 2 iterations of the application**

- Reuse as much code as possible

Expand All @@ -104,10 +104,10 @@ During the **second iteration**, which was recently held, Pedro Silva shared the

- Replace/shim functionality that was lost from removing dependencies

Here is the list of dependencies to packages on CRAN, those that worked are colored green, those that were removed are marked in orange. We ended up with just 3 problematic dependencies (bold).
Here is the list of dependencies to packages on CRAN; those that worked are colored green, and those that were removed are marked in orange. We ended up with just 3 problematic dependencies (bold).
```
| | |
|------------------------------------|------------------------------------|
|-------------------------------------------|-------------------------------------------|
| [library(config)]{style="color:orange"} | [library(reactable)]{style="color:green"} |
| **library(cowplot)** | [library(rhino)]{style="color:orange"} |
| [library(dplyr)]{style="color:green"} | [library(rtables)]{style="color:green"} |
Expand All @@ -121,11 +121,12 @@ Here is the list of dependencies to packages on CRAN, those that worked are colo
| [library(markdown)]{style="color:green"} | [library(Tplyr)]{style="color:green"} |
| [library(pkgload)]{style="color:green"} | [library(utils)]{style="color:green"} |
| [library(purrr)]{style="color:green"} | [library(visR)]{style="color:green"} |
```

Issues with library(cowplot):

- Some issue with low-level dependencies when deployed
- Some issues with low-level dependencies when deployed

Solution:

Expand Down Expand Up @@ -153,23 +154,22 @@ Solution:

3. **Leverage shinylive and httpuv to export and serve the application**

a. **Shinylive can help streamline the export process**
a. Shinylive can help streamline the export process

i. **Problems**
i. Problems

1. **shiny.live won't let us have non-R files in the application directory - this is an outstanding bug that George asked us to raise an issue for.**
1. shiny.live won't let us have non-R files in the application directory - this is an outstanding bug that George asked us to raise an issue for.

2. **We wouldn't be able to run the application as a traditional shiny app**
2. We wouldn't be able to run the application as a traditional shiny app.

ii. **Solution:**
ii. Solution:

```
1. **Custom build script**
```
1. Custom build script


b. **{httpuv} can help serve the application**
b. {httpuv} can help serve the application

i. **{httpuv} would run natively on a machine to serve the Shiny app**
i. {httpuv} would run natively on a machine to serve the Shiny app

#### Application Structure

Expand All @@ -191,9 +191,9 @@ Some of the issues and solutions found at the very beginning:
i. Shim and used functionality
ii. Use a simple tab system for the UI structure

The FDA were previously told that the shiny application being prepared for the Pilot 4 submission would not be a 1 to 1 mapping from the previous one submitted for the Pilot 2 due to certain constraints such as {teal} not being on CRAN; however, this didn't represent a problem for them since they would mainly like to test the technology.
The FDA was previously told that the shiny application being prepared for the Pilot 4 submission would not be a 1 to 1 mapping from the previous one submitted for the Pilot 2 due to certain constraints such as {teal} not being on CRAN; however, this didn't represent a problem for them since they would mainly like to test the technology.

Pedro Silva, one of the engineers working on the development of this app mentioned **"While WebR is still in development, it shows tremendous promise! The loading is definitely still a pain point (over 100mb to set up the environment!) but it will only get better moving forward."**
Pedro Silva, one of the engineers working on the development of this app, mentioned **"While WebR is still in development, it shows tremendous promise! The loading is definitely still a pain point (over 100mb to set up the environment!) but it will only get better moving forward."**

#### Containers

Expand Down Expand Up @@ -234,18 +234,18 @@ Below is the dockerfile (recipe) for the container:

# Next Steps

The next steps are waiting for the review of the 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. 
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. 

1. Submission to FDA
2. Rhino Compatibility

![](images/rhino.png){fig-align="center" width="161"}

Appsilon is working on the side with Rhino compatibility, eventually we might be able to just add this framework into the Pilot 4 application.
Appsilon is working on the side with Rhino compatibility; eventually, we might be able to just add this framework into the Pilot 4 application.

3. {teal}

This and other packages might be on CRAN soon. We could incorporate them after that, replacing the shims created for this version
This and other packages might be on CRAN soon. We could incorporate them after that, replacing the shims created for this version.

4. Boot Time

Expand Down
Loading