Table 1 |
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Listed are the ISL parameters and the values used for this work. |
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Parameter |
Value |
Description |
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StepsPerCycle |
2 |
# of model steps in 1 simulation cycle |
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SSTypeRatio |
0.550 |
Ratio of short, wide SS to long, narrow SS |
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DirSinCirc |
24 |
Width of short, wide SS |
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DirSinLenAlpha |
1.000 |
Gamma distribution shape parameter |
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DirSinLenBeta |
0.085 |
Gamma distribution scale parameter |
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DirSinLenShift |
0.000 |
Scalar shift parameter |
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TortSinCirc |
10 |
Width of long, narrow SS |
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TortSinLenAlpha |
8.000 |
Gamma distribution shape parameter |
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TortSinLenBeta |
0.075 |
Gamma distribution scale parameter |
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TortSinLenShift |
-10.000 |
Scalar shift parameter |
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SinusoidTurbo |
0.250 |
Ratio of forward to zero bias for COMPOUND random walk |
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CoreFlowRate |
1 |
# SS grid points per cycle COMPOUND moves in the Core and the BILECANAL |
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BileCanalCirc |
1 |
Thickness of the BILECANAL in SS grid points |
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S2EJumpProb |
0.850 |
Likelihood a COMPOUND will move from Space A to Space B |
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E2SJumpProb |
0.150 |
Likelihood a COMPOUND will move from Space B to Space A |
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E2DJumpProb |
0.850 |
Likelihood a COMPOUND will move from Space A to Space C |
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D2EJumpProb |
0.150 |
Likelihood a COMPOUND will move from Space C to Space B |
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ECDensity |
0.900 |
Fraction of Space B points filled with ENDOTHELIAL CELLS |
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HepDensity |
0.900 |
Fraction of Space C points filled with HEPATOCYTES |
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BindersPerCellMin/Max |
125/125 |
Uniformly distributed # of BINDER objects in each CELL |
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MetabolismProb |
0.200 |
Likelihood a bound COMPOUND will be METABOLIZED |
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SoluteBindingProb |
0.750 |
Likelihood an INTRACELLULARCOMPOUND will be bound |
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SoluteBindingCycles |
15 |
# of cycles a COMPOUND is bound |
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SoluteScale |
1.0 |
Scaling from ISL to wet-lab dose fraction |
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MembraneCrossing |
No/Yes |
Whether COMPOUND crosses CELL membranes |
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BileRatio |
0%/50% |
Percent of COMPOUND that goes back into CELL vs. bile |
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Dosage |
5,000 |
Generate and insert this many COMPOUND objects |
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DosageCycle |
2 |
Simulation cycle at which to inject the COMPOUND |
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Ropella and Hunt BMC Systems Biology 2010 4:168 doi:10.1186/1752-0509-4-168 |
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