CREATING_MODEL_REPOSITORY.md

Creating a new model repository.

1. If you are an OSP community member: create a model repository as described in step 3.

2. Otherwise (in case you are not an OSP community member): post an Issue in the Forum and ask to create an empty model repository for you. For this, please provide the information below (s. step 3 for the details).

   • name of your model (e.g. Midazolam, check if already exists, otherwise use another name)

   • short description of the model repository (e.g. Whole-body PBPK model of midazolam as CYP3A4 DDI victim drug)

   • repository topics (e.g. pbpk, pbpd, ddi, pediatrics, ...)

   As soon as an empty model repository is created: continue with step 4.

3. Creating a model repository:

   • Please create one repository per substance (where possible)

   • Under Repository template: select Open-Systems-Pharmacology/Evaluation-plan-template (s. the screenshot below)

   • Repository name: <Substance>-Model (e.g. Midazolam-Model)

   • (Optional) short description of the Repository

   • Set repository type to Public
     
     

     

   • Define Repository-topics:

     • Mandatory topic for model repositories: osp-model
     • Further topics: Optional. Topics are free text; however try to use predefined topics if available. Some predefined topics are:
       • pbpk
       • pbpd
       • pk-sim
       • mobi
       • ddi
       • pediatrics

4. Create a so called Fork of the OSP Model repository. This will create your own personal copy of the OSP repository, where you can upload and modify files (this copy is still public and visible to everybody). S. https://guides.github.com/activities/forking/ for more details.

5. To upload files in your fork, just click on the “upload files” button and select your local files (this works for files <=25 MB. For files between 25 and 100 MB use the command line )

   • If you need to modify a file: you can do it locally and simply upload the modified file version. It will automatically overwrite the previous version.
     
     

6. Every model repository must contain project snapshots of all PK-Sim projects (what is a "PK-Sim snapshot") and a description of the repository in the README.md file (s. step 7.). E.g.

• The folder Evaluation in the screenshot above contains a template for creating a Model Evaluation plan (s. Qualification and Model Evaluation plans for details). Adding a Model Evaluation plan is optional, but highly recommendable. This step is a MUST for every model which should be added to the OSP PBPK Model Library.
  • Some examples :
    • Erythromycin evaluation plan (Evaluation-Report: s. here)
    • Sildenafil evaluation plan (Evaluation-Report: s. here)

7. README.md is written in the Markdown-Format (s. here and here for details.). It can be edited directly on GitHub in your Fork of a model repository when you click on the Edit button.

   • Some README examples
     • Alfentanil-Model README
     • Glucose-Insulin-Model README

8. When you are finished with uploading files and Readme in your fork of the model repository, you must create a so called Pull Request (PR). This is a proposal for the OSP to integrate your work back into the the original repository. For this, click on the “Code” tab first and then on “New pull Request”.

9. On the next page, click on "Create Pull Request".

10. On the next page you can optionally select reviewers for your PR. Finally, click on “Create Pull Request” button.

Now somebody from the OSP maintainers team can integrate your work backt into the OSP (or ask you for changes if e.g. something needs to be modified before the PR can be accepted).