PhysiCellModelManager.jl

PhysiCellModelManager.jl (PCMM) is a Julia package for running large PhysiCell simulation campaigns. It manages the inputs, variations, and databases so you can define a parameter sweep, sensitivity analysis, or calibration once and let PCMM organize, deduplicate, and reproduce the runs.

New here? Start with Installation, then Your first project.

Where do I look?

Getting set up

I want to…	Go to
Install the package and run my first simulations	Installation, Your first project
Set up a reproducible Julia environment	Julia environments
Bring in an existing PhysiCell project	Importing a project

Building and varying a model

I want to…	Go to
Change parameter values across runs	Varying parameters, XML path helpers
Vary parameters together or under constraints	CoVariations, LatentVariations
Add an intracellular (ODE) model	Intracellular inputs

Getting results out

I want to…	Go to
Plot or query results	Analyzing output, Querying parameters
Compute quantities while runs are still in flight	Post-processing and quantities of interest
Measure spatial structure or cell–cell contacts	Pair correlation function, Graph analysis
Turn snapshots into a movie	Movies
Label a batch of runs and find them again later	Tagging and recovery

Analyzing and fitting

I want to…	Go to
Find out which parameters matter most	Sensitivity analysis
Fit a model to data with ABC-SMC	Calibration

Reference and troubleshooting

I want to…	Go to
Copy-paste a recipe	Examples
Look up a function's signature	the Index (all exported symbols)
Understand where PCMM puts things on disk	Data directory structure, Project configuration
Open a project in the PhysiCell GUI	Using PhysiCell Studio
Upgrade an older project's database	Database upgrades
Troubleshoot something	Known limitations, Best practices

Issues

Have a problem? First check Known limitations and Best practices. If it persists, please open an issue here.