- the configuration of simulation setup that shall be simulated (mostly referred to as main configuration file) and
- the configuration of technical details of the simulation (mostly referred to as technical file)
If not explicitly stated otherwise, all time values are given in days.
Technical configurationThe technical configuration file is structured as follows:
<technical> <duration> </duration> <timeStepsForSaving> </timeStepsForSaving> <debug-mode> </debug-mode> </technical>
||Defines the time span the simulation shall cover. Please also adjust the value for the tag
Defines the interval for saving the current status of the simulated system. This value,
together with the duration, directly influences the size of the resulting output file.
For fast growing tumours use small values to keep track of the progress. For slowly growing
tumours user bigger values (e.g. 10-30) to avoid unnecessary big output files.
Enables or disables the debug mode. In the debug mode more information are printed during
the simulation. Valid values are
Main configurationThe main configuration file is structured as follows:
<metastatic-Cascade> is the main tag and surrounds the whole
configuration. It includes the sections
compartments and the optional
globalTreatments which are described in detail below.
functions section the growth functions
and the colonization rates are defined.
For parametrization details of each function or an example configuration of the
functions section please see the function page.
distributions section the distributions
For parametrization details of each distribution or an example configuration of the
distributions section please see the distribution page.
hostOrgans section the different host organs for the primary tumor and metastases are
defined. Please note that the bloodstream is also handled as an organ. For parametrization details
please see the host organ page.
compartmentTypes section the characteristics of a discrete compartment are defined
discreteCompartmentType element including the set off possible event actions that may occur
in a discrete compartment. By using compartment types the same characteristics can be applied for
multiple discrete compartments. For parametrization details please see the
compartment types and event actions page.
compartments section the initial compartments that are present at the start of
the simulation are defined. At least the primary tumor has to be defined. Mostly also the bloodstream
is defined in this section. Metastases are not defined in this section since they are created
during the course of the simulation according to the parametrized characteristics. For parametrization details
please see the compartments page.
globalTreatments section therapies such as chemotherapy, external beam radiation,
radioimmunotherapy and radioembolization are parametrized. For details please see the
global treatments page.