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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.