From: Toward modular biological models: defining analog modules based on referent physiological mechanisms
Parameter name | Type/Range | Example | In ISL? | Description |
---|---|---|---|---|
Simulation control parameters | Â | |||
seed | natural | 12345 | Yes | Random number generator seed. |
cycleLimit | natural | 120 | Yes | Cycles after which to stop the simulation. |
monteCarloTrials | natural | 16 | Yes | Number of Monte Carlo trials to execute. |
Whole model parameters | Â | |||
dosage | natural | 10000 | No | Number of Solutes to administer at the start of the simulation. |
pExitMedia | [0.0,1.0] | 0.15 | No | Random draw from U(0,1) ≤ this value determines whether a Solute can move from MediaSpace to CellSpace. |
pExitCell | [0.0,1.0] | 1.0 | No | Random draw from U(0,1) ≤ this value determines whether a Solute can move from CellSpace to MediaSpace. |
scale | integer | 50 | No | Number of Solutes that can fit in one grid point in CellSpace. |
hepDensity | [0.0,1.0] | 0.9 | Yes | Fraction of grid points in CellSpace that contain a Hepatocyte. |
Hepatocyte parameters | Â | |||
pBind | [0.0,1.0] | 0.1 | Yes | Random draw from U(0,1) ≤ this value causes a Binder to bind a Solute. |
bindersPerCellMin | integer | 4 | Yes | Minimum for a uniform random draw setting initial number of Binders in a particular Cell. |
bindersPerCellMax | natural | 8 | Yes | Maximum for a uniform random draw setting initial number of Binders in a particular Cell. |
bindCycles | natural | 2 | Yes | Number of simulation cycles a Solute stays bound to a Binder. |
Solute-specific parameters | Â | |||
membraneCrossing | boolean | TRUE | Yes | Indicates whether this Solute type can partition into Cells. |
pMetabolize | [0.0,1.0] | 0.1 | Yes | Random draw from U(0,1) ≤ this value causes an Enzyme to metabolize the Solute to which it is bound. |
tag | string | Metabolite | Yes | Name for this type of Solute (e.g. Drug, Metabolite). |
ratio | [0.0,1.0] | 0.5 | Yes | Fraction of this type of Solute to create. |
Induction/elimination parameters | Â | |||
eiThresh | natural | 1 | Yes | Threshold above which the induction accumulator triggers an induction event. |
eiRate | ≥ 0.0 | 0.05 | Yes | Rate at which Enzymes can be created. |
eiResponse | ≥ 0.0 | 0.25 | Yes | Number of Enzymes to induce when an induction event is triggered. |
elThresh | natural | 1 | Yes | Threshold above which the elimination accumulator triggers an elimination event. |
elRate | ≥ 0.0 | 0.05 | Yes | Rate at which Enzymes can be destroyed. |
elResponse | ≥ 0.0 | 0.25 | Yes | Number of Enzymes to eliminate when an elimination response is triggered. |