Table 2.
Global and state variables used in the ABM.
| Variable name | Variable type | Functionality | Value and source |
|---|---|---|---|
| Name | State | Identifies the molecular agent (e.g. Raf, Runx2 or OPN) | — |
| ID | State | Identifies the molecular agent sequential order | — |
| State | State | Activation state | Adapted from the literature and agent dependent* |
| Cartesian coordinates | State | Expresses the agents coordinates in Cartesian system | Assigned randomly at t0 to comply with the homogeneous distribution of molecules within a well-mixed cell72,76 |
| Radian coordinates | State | Expresses the agents coordinates in radian system | |
| ACS* | State | Timer to account for feedback loops and thus control dormancy phase | Adapted from the literature and agent dependent* |
| interaction radius (iradius) | State | The radius to allow for interactions between two agents | Adapted from the literature and agent dependent70,* |
| Cell radius | Global | Define the outer cell boundary | 10 µm77,78 |
| Nuclear radius | Global | Defines the nucleus cytosol boundary | 4 µm78 |
| Time-step | Global | Every time-step was calibrated to 1 second to account for molecular events | 1 s per iteration69 |
The table lists the common variables shared by all agents, however, majority of agents have customised variables, which were listed and can be found in the UniDrive. *For customised variables for specific agents see UniDrive.