Your first project

Once PhysiCellModelManager.jl is installed (see Installation), this page walks you from an empty folder to your first simulations. Skim Best practices first.

Create a project

Load the package and create a project:

julia> using PhysiCellModelManager
julia> createProject() # uses the current directory by default

This creates three folders inside the project folder: data/, PhysiCell/, and scripts/. Pass a path to createProject to use a different folder. See Data directory structure for what lives in data/.

Note

A PhysiCellModelManager.jl project is distinct from PhysiCell's sample_projects and user_projects.

Already have a PhysiCell project to bring in? See Importing a project.

Run your first trial

createProject puts a single script at scripts/GenerateData.jl (the folder and file names are convention — rename them freely). Run it from the shell:

julia scripts/GenerateData.jl

You can also run it from the REPL.

To parallelize the runs, set PCMM_NUM_PARALLEL_SIMS to the number of parallel simulations:

export PCMM_NUM_PARALLEL_SIMS=9
julia scripts/GenerateData.jl

Or as a one-off:

PCMM_NUM_PARALLEL_SIMS=9 julia scripts/GenerateData.jl

Run the script a second time: no new simulations run. PhysiCellModelManager.jl matches existing simulations before running new ones, so re-running a script is cheap. Use the use_previous keyword argument to override this.