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Table 1 ISHC parameters details and descriptions, including whether that parameter also exists in the ISL

From: Toward modular biological models: defining analog modules based on referent physiological mechanisms

Parameter name Type/Range Example In ISL? Description
Simulation control parameters  
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  
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  
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  
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  
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.