Pirana can be set up to recognize and access existing Darwin installations and execute Darwin runs locally or remotely. Both local and remote host definitions and profiles are required and can be created using the Pirana Settings dialog.
Local searches use the Python interpreter path from the Darwin settings page, the Rscript path from the Software integration page, the nmfe path from the Darwin profile page, and the NLME Engine and GCC directory paths from the NLME page.
Remote searches require that the Python interpreter, Rscript, and either nmfe script or NLME Engine directory paths be set as part of the profile (see “Darwin profiles”). If the NLME Engine directory is set, the GCC directory path must be set as well.
Preparing for Darwin searches in Pirana
Prior to using Darwin searches in Pirana, there are some installation and verification steps required.
Install Python.
The pyDarwin-Certara Python package is supported on Python 3.10+. The steps below describe installing version 3.12.
Go to the python.org website and select the latest release version of Python 3.12 from the Downloads table of specific releases.
At the bottom of the information page, click Windows installer (64-bit) to launch the installer.
On the first screen of the installer, check the Add python.exe to PATH box.
Note the default installation location is C:\Users\<username>\AppData\Local\Programs.
Click Install Now.
On the “Setup was successful” screen, press Close.
Verify that Python was correctly installed and configured in the PATH.
Use the search field in the taskbar to look for the list of environment variables in your account.
In the Environment Variables dialog, double-click Path in the “User variables” list.
Confirm that Python 3.12 is listed in the Edit environment variable dialog. (Look for …\Python\Python312\Scripts\ and …\Python\Python312\.)
Press OK and then Cancel to close the two dialogs.
Launch a Command Prompt window and enter the python -V command.
It should return Python followed by the version number you just installed.
Install jsonlite.
Darwin search functionality in Pirana requires an additional R dependency in jsonlite. Ensure that the jsonlite package has been installed in the R library using the command in R/RStudio:
install.packages("jsonlite")
Create an empty folder called venv (virtual environment).
Best practice is to place the new folder in \Documents or at least a level above your project.
In Pirana, select File > Settings and click Darwin in the left list.
Click 
to download pyDarwin from the pip repository.
In the file browser, navigate to and select the venv folder created earlier.
A virtual environment is created inside the empty folder by copying the installed version of Python and creating a self-contained library for all Python packages and dependencies installed with pyDarwin. This allows the version of Python and dependencies used in one project to be insulated from Python versions and dependencies used in other projects. The virtual environment only needs to be set up once, when installing pyDarwin.
Once installation completes, close the text window.
The path to the Python executable in the virtual environment folder is displayed in the Python interpreter for local searches field. The venv folder created earlier is now populated, with pyDarwin being in the …venv/Lib/site-packages subfolder.
Install Darwin Reporter in the R library using the command in R/RStudio:
install.packages("Certara.DarwinReporter", repos = c("https://certara.jfrog.io/artifactory/certara-cran-release-public/", "https://cloud.r-project.org"), method = "libcurl")
The Certara.DarwinReporter R package provides a Shiny application integrated within Pirana that is used to analyze and report Darwin search results.