Helper functions to define targets

For each of the varied input types, pcvct has a helper function to create the XML path.

Varying config parameters

The configPath function can be used to create the XML path to almost^[1] any parameter in the configuration file intuitively. See Config XML paths for an exhaustive explanation of the available tokens. Here are some simple examples to get you started:

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

The rulePath function can help start the XML path to rules parameters. It does not infer the full path from tokens like configPath, but relies on the user knowing the structure of the rules XML file. The first argument is the cell type and the second argument is the behavior. The remaining arguments are the remaining entries in the XML path. Here are some examples:

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

pcvct supports an XML-based initialization of cell locations using PhysiCellCellCreator.jl. See the documentation of that package for details on how to create the XML file. Use pcvct.createICCellXMLTemplate to create a template XML file and automatically add it to the database. From there, you can edit it directly (though as per Best practices do not edit after simulations are created that rely on it).

To vary parameters in this XML file, the icCellsPath function can be used. The signature is as follows:

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

PhysiCellCellCreator.jl supports carveouts that can be used to not place cells within the given patches. These are contained in a child element of the patch element and their parameters can be varied using the following signature:

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

Varying initial ECM parameters

pcvct supports an XML-based initialization of ECMs using PhysiCellECMCreator.jl. See the documentation of that package for details on how to create the XML file. Use pcvct.createICECMXMLTemplate to create a template XML file and automatically add it to the database. From there, you can edit it directly (though as per Best practices do not edit after simulations are created that rely on it).

To vary parameters in this XML file, the icECMPath function can be used. The signature is as follows:

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".