Using PhysiCell Studio

See PhysiCell-Studio. Within PhysiCellModelManager.jl, PhysiCell Studio is for visualizing output (the Plot tab) and inspecting model parameters (the other tabs).

Do not use the Run tab in PhysiCell Studio — it may delete simulation data.

See Editing in PhysiCell Studio for editing the configuration and rules files.

Setting paths

Environment variables

First tell PhysiCellModelManager.jl where your python executable and PhysiCell Studio folder are. On macOS/Linux, add 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

Alternatively, pass the paths as keyword arguments to runStudio (see below). It remembers them for the session, so you only pass them once.

Launching PhysiCell Studio

First, launch julia in a new shell session and initialize the project:

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

runStudio opens Studio on the specified simulation using temporary configuration and rules files, so edits are lost when Studio closes — remember, this is the output of a simulation that already ran. Save the configuration with File > Save as and the rules from the Rules tab. The PhysiCell 1.14.1 behavior of copying over initial-conditions files is not yet supported; see Known limitations.