XML path helpers

Each varied input type has a helper function that builds its XML path.

Varying config parameters

configPath builds the XML path to almost^[1] any configuration parameter from intuitive tokens. See Config XML paths for the full token reference. Some examples:

configPath("max_time")
configPath("full_data_interval")
configPath(<substrate_name>, "diffusion_coefficient")
configPath(<cell_type>, "cycle", "rate", 0)
configPath(<cell_type>, "speed")
configPath(<cell_type>, "custom", <tag>)
configPath("user_parameters", <tag>)

Varying rules parameters

rulePath builds the XML path to rules parameters. Unlike configPath, it does not infer the path from tokens — you supply the cell type, the behavior, then the remaining XML-path entries directly:

rulePath(<cell_type>, <behavior>, "increasing_signals", "max_response")
rulePath(<cell_type>, <behavior>, "decreasing_signals", "max_resposne")
rulePath(<cell_type>, <behavior>, "increasing_signals", "signal:name:<signal_name>", <tag>)
rulePath(<cell_type>, <behavior>, "decreasing_signals", "signal:name:<signal_name>", "reference", "value")

Varying initial cell parameters

PhysiCellModelManager.jl initializes cell locations from XML via PhysiCellCellCreator.jl (see its docs for the file format). Use PhysiCellModelManager.createICCellXMLTemplate to create a template and register it in the database; edit it directly afterward (but per Best practices, not after dependent simulations exist).

Vary its parameters with icCellsPath:

icCellsPath(<cell_type>, <patch_type>, <patch_id>, <tag>)

PhysiCellCellCreator.jl also supports carveouts (a child element of the patch) that exclude cells from a region. Vary their parameters with:

icCellsPath(<cell_type>, <patch_type>, <patch_id>, <carveout_type>, <carveout_id>, <tag>)

Varying initial ECM parameters

PhysiCellModelManager.jl initializes ECMs from XML via PhysiCellECMCreator.jl (see its docs for the file format). Use PhysiCellModelManager.createICECMXMLTemplate to create a template and register it in the database; edit it directly afterward (but per Best practices, not after dependent simulations exist).

Vary its parameters with icECMPath:

icECMPath(<layer_id>, <patch_type>, <patch_id>, <tag>)

Or in the case of using a patch type "ellipse_with_shell" there are additional parameters for the two (or three) subpatches:

icECMPath(<layer_id>, "ellipse_with_shell", <patch_id>, <subpatch>, <tag>)

where <subpatch> is one of "interior", "shell", or "exterior".