Creation of Model Evaluation / Qualification Reports directly on GitHub

Preparation

• Fork this repository into your GitHub user account (if you have not done so yet).

• Enable Workflows on your forked repository

  

• [OPTIONAL] Synchronize the main branch of your fork with the parent OSP repository if required
  (see Syncing a fork in the GitHub documentation for details).

Notes

• Do not use Excel to edit and save CSV files. Use a text editor only.

How to create model evaluation reports

1. Create a new branch (e.g. my-reports) from the main branch of your fork.
2. Define the models by updating models.csv (see the Models section below for details)
   • Once you are finished, push the new branch to your fork and verify that the check Validate models.csv was successful!
3. [OPTIONAL] Adjust the OSP environment and tools by updating tools.csv
   (see the Tools section below for details)
   • In case of modifications: verify that the check Validate tools.csv was successful!
4. Go to the GitHub Action: Create evaluation reports and projects
   
   

   • Click the Run workflow button

   • Select the branch defined in the first step (for instance, my-reports)

   • [OPTIONAL] Adjust the commit message that will appear later in the created pull request
     (see the What to do when reports are created section below).

   • Click the green Run workflow button

     

How to create qualification reports

1. Create a new branch (e.g. my-reports) from the main branch of your fork.
2. Define the qualifications by updating qualifications.csv (see the Qualifications section below for details)
   • Once you are finished, push the new branch to your fork and verify that the check Validate qualifications.csv was successful!
3. [OPTIONAL] Adjust the OSP environment and tools by updating tools.csv
   (see the Tools section below for details)
   • In case of modifications: verify that the check Validate tools.csv was successful!
4. Go to the GitHub Action: Qualification Reports
   • Click the Run workflow button
   • Select the branch defined in the first step (for instance, my-reports)
   • [OPTIONAL] Adjust the commit message that will appear later in the created pull request
     (see the What to do when reports are created section below).
   • Click the green Run workflow button

What to do when reports are created

When qualification reports are created, pull requests (PRs) are created (one PR for each qualification report) toward the branch defined in the first step (for instance, my-reports).
These pull requests allow users to review report updates and adopt the new version. For each created PR:

• Close and reopen the PR: this will trigger the automated checks (e.g. links and cross-references) of the created report.
• If you have a GitHub Copilot license: assign Copilot as a PR reviewer (Copilot will then check the report as well)

Models

The models.csv file indicates which models should be run and qualified. The header includes the following fields:

• Execute: If TRUE, run the qualification. If FALSE, skip the qualification.
• Repository name: Name of the GitHub OSP repository from which to get the model, e.g.
  7E3-Model for https://github.com/Open-Systems-Pharmacology/7E3-Model
• Released version: Tag version of the model repository release, e.g. 1.0.
  Alternatively, use a branch name of the model repository (e.g. main).
• Snapshot name: Name of the snapshot (.json) file, e.g.
  7E3 in https://github.com/Open-Systems-Pharmacology/7E3-Model/7E3.json
• Folder name: Name of the target folder where the model evaluation report (and the project file(s)) should be created.
• Workflow name: Path of the workflow R script that creates the function to run the qualification if not default.

Tip

Leave the cell blank if the default path, evaluation/workflow.R, is used (this path is case insensitive).

• Additional projects: URL(s) of additional project snapshots to export as pksim5 projects, e.g. Propofol-Pediatrics/refs/tags/v1.0/Propofol-Pediatrics.json

Tip

If multiple projects are exported, they need to be separated by a pipe character: |, e.g. X-Pediatrics.json|Y-Pediatrics.json

Qualifications

The qualifications.csv file indicates which qualification plans should be processed. The header includes the following fields:

• Execute: If TRUE, run the qualification. If FALSE, skip the qualification.
• Repository name: Name of GitHub OSP repository from which to get the qualification plan, e.g. Qualification-CKD for
  https://github.com/Open-Systems-Pharmacology/Qualification-CKD
• Released version: Tag version of the qualification plan repository release, e.g. 1.0.
  Alternatively, use a branch name of the qualification plan repository (e.g. main).
• Workflow name: Path of the workflow R script that creates the function to run the qualification if not default.

Tip

Leave the cell blank if the default path, Qualification/workflow.R, is used (this path is case insensitive).

• Folder name: Name of the target folder where the qualification report should be created.

Tools

The tools.csv file indicates the software and versions to be installed in the environment before running model qualifications. If a link is defined in the URL column, the installation uses the software from that link as is instead of resolving from the version. Please ensure compatibility between their versions. The available tools to be installed are listed below:

• ospsuite-R : R package providing functionality for loading, manipulating, and simulating models created in the Open Systems Pharmacology Software tools PK-Sim and MoBi.
• Reporting Engine: R package providing a framework in R to design and create reports evaluating PBPK models developed in the Open Systems Pharmacology ecosystem.
• RUtils: R package providing utility functions for Open Systems Pharmacology R packages
• TLF: R package providing an object-oriented framework to create tables and figures, which are used by R packages in the Open Systems Pharmacology ecosystem
• DEPRECATED rClr: R package for accessing .NET. This package has been deprecated in favor of {rSharp}.
• rSharp: R package providing access to .NET libraries from R. It allows users to create .NET objects, access their fields, and call their methods
• Qualification Runner: Qualification runner responsible for managing a qualification workflow
• Qualification Framework: Enables automated validation of various scenarios (use-cases) supported by the OSP platform
• PK-Sim: Portable version of the comprehensive software tool for whole-body physiologically based pharmacokinetic modeling

Code of conduct

Everyone interacting in the Open Systems Pharmacology community (codebases, issue trackers, chat rooms, mailing lists etc...) is expected to follow the Open Systems Pharmacology code of conduct.

Contribution

We encourage contribution to the Open Systems Pharmacology community. Before getting started please read the contribution guidelines. If you are contributing code, please be familiar with the coding standards.

License

GPLv2 License.