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Using PhysiCell Studio

See PhysiCell-Studio. Using PhysiCell Studio within PhysiCellModelManager.jl is designed for visualizing output in the Plot tab and observing model parameters in the remaining tabs.

Do not use the Run tab in PhysiCell Studio as this may delete simulation data.

See below for how to edit the configuration and rules files in studio.

Setting paths

Environment variables

You must first inform PhysiCellModelManager.jl where your desired python executable is and the PhysiCell Studio folder. The recommended way to do this on macOS/Linux is to add the following two lines to your shell environment file (e.g. ~/.bashrc or ~/.zshenv):

export PCMM_PYTHON_PATH=/usr/bin/python3
export PCMM_STUDIO_PATH=/home/user/PhysiCell-Studio

If your python executable is on your PATH, you can set PCMM_PYTHON_PATH=python3, for example.

After making these changes, make sure to source the file to apply the changes:

source ~/.bashrc

Or open a new terminal window.

On Windows, the simplest way to set these is to use the GUI for setting environment variables.

Troubleshooting: If you are having trouble launching PhysiCell Studio...

  • PCMM_PYTHON_PATH must point to a valid python executable
  • PCMM_STUDIO_PATH must point to the PhysiCell Studio folder, not the studio.py file
  • the ~ character is not expanded when in quotes, so export PCMM_STUDIO_PATH="~/PhysiCell-Studio" will not work

Using keyword arguments

If you prefer not to set these environment variables, you can pass the paths as keyword arguments to the runStudio function. It will remember these settings during the session, so you only need to pass them once. See below for the function signature.

Launching PhysiCell Studio

First, launch julia in a new shell session and make sure the project is initialized by running:

using PhysiCellModelManager

Note: If you have already loaded the package in this session, run initializeModelManager if you need to initialize the project.

As soon as the simulation has begun (so that its PhysiCell-generated output folder is created and populated), you can launch PhysiCell Studio. If you set the environment variables, you can run the following command for a simulation with id sim_id::Integer:

julia> runStudio(sim_id)

If you did not set the environment variables, you can run the following command:

julia> runStudio(sim_id; python_path=path_to_python, studio_path=path_to_studio)

Editing in PhysiCell Studio

When you run the runStudio function, PhysiCell Studio will open with the simulation you specified using temporary files for the configuration and rules. Any edits to these in studio will be lost when the studio is closed. Remember: this is the output of a simulation that already ran. Use the File > Save as dropdown to save the configuration file. Use the Rules tab to save the rules file. Note: the recent changes in PhysiCell 1.14.1 copying over the initial conditions files are not yet supported by this. See Known limitations for more information.