RT Journal Article
SR Electronic
T1 Determining a reasonable range of relative numerical tolerance values for simulating deterministic models of biochemical reactions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 256214
DO 10.1101/256214
A1 Yang, Ming
A1 Yang, Louis Z.
YR 2018
UL http://biorxiv.org/content/early/2018/01/29/256214.abstract
AB What values of relative numerical tolerance should be chosen in simulation of a deterministic model of a biochemical reaction is unclear, which impairs the modeling effort since the simulation outcomes of a model may depend on the relative numerical tolerance values. In an attempt to provide a guideline to selecting appropriate numerical tolerance values in simulation of in vivo biochemical reactions, reasonable numerical tolerance values were estimated based on the uncertainty principle and assumptions of related cellular parameters. The calculations indicate that relative numerical tolerance values can be reasonably set at or around 10−4 for the concentrations expressed in ng/L. This work also suggests that further reducing relative numerical values may result in erroneous simulation results.