GitHub

Data directory structure

createProject builds this structure for you under project-dir. This page documents what each folder holds so you can add or edit inputs by hand.

project-dir/
├── data/
│   └── inputs/
│       ├── configs/
│       ├── custom_codes/
│       ├── ics/
│       │   ├── cells/
│       │   ├── dcs/
│       │   ├── ecms/
│       │   └── substrates/
│       ├── intracellulars/
│       ├── rulesets_collections/
...

Each terminal subdirectory under data/inputs/ holds input folders whose names you choose. The examples below use "baseline", but any name works.

Configs

Place your base configuration file at data/inputs/configs/baseline/PhysiCell_settings.xml.

Custom codes

Place the following in data/inputs/custom_codes/baseline/, exactly as used in a PhysiCell project:

  • main.cpp
  • Makefile
  • custom_modules/

PCMM compiles into this folder as well, adding the compilation logs, macros.txt, and a pcmm_build/ subfolder holding one executable per PhysiCell version it has built for (pcmm_build/project_<version>). These are generated files, ignored by the .gitignore createProject writes; delete pcmm_build/ to force a fresh build.

Rulesets collections

Place your base ruleset collection at data/inputs/rulesets_collections/baseline/base_rulesets.csv (skip this if your project has no rules). You may instead place an XML file here, created from a CSV with PhysiCellXMLRules.jl.

Important: variations must target the XML version. After initializeModelManager, any folder with base_rulesets.csv is populated with a base_rulesets.xml to reference for XML paths.

Intracellulars

Place a single intracellular.xml at data/inputs/intracellulars/baseline/, with root children cell_definitions and intracellulars. Only libRoadRunner (ODEs) is currently supported; see sample_projects_intracellular/combined/template-combined for an example and Intracellular inputs for details.

ICs

These folders are optional. For each initial condition, add a subfolder. For example, with two initial cell-position conditions random_cells.csv and structured_cells.csv, data/inputs/ics/cells/ looks like:

cells/
├── random_cells/
│   └── cells.csv
└── structured_cells/
    └── cells.csv

Note: place each file in its folder and rename it to cells.csv.

Proceed similarly for dcs/, ecms/, and substrates/, renaming the files to dcs.csv, ecm.csv, and substrates.csv.

IC cells

To generate cells.csv from geometries, place a cells.xml (see PhysiCellCellCreator.jl) in place of the cells.csv. You can vary it just as for config and rulesets_collection.

IC ecm

To generate ecm.csv from a defined structure, place an ecm.xml (see PhysiCellECMCreator.jl) in place of the ecm.csv. You can vary it just as for config and rulesets_collection.