configData: Configuration Data
In lusystemsbio/sRACIPE: Systems biology tool to simulate gene regulatory circuits

configData

R Documentation

Configuration Data

Description

It contains simulation parameters like integration method (stepper) and other lists or vectors like simParams, stochParams, hyperParams, options, thresholds etc. The list simParams contains values for parameters like the number of models (numModels), simulation time (simulationTime), step size for simulations (integrateStepSize), when to start recording the gene expressions (printStart), time interval between recordings (printInterval), number of initial conditions (nIC), output precision (outputPrecision), tolerance for adaptive runge kutta method (rkTolerance), parametric variation (paramRange). The list stochParams contains the parameters for stochastic simulations like the number of noise levels to be simulated (nNoise), the ratio of subsequent noise levels (noiseScalingFactor), maximum noise (initialNoise), whether to use same noise for all genes or to scale it as per the median expression of the genes (scaledNoise), ratio of shot noise to additive noise (shotNoise). The list hyperParams contains the parameters like the minimum and maximum production and degration of the genes, fold change, hill coefficient etc. The list options includes logical values like annealing (anneal), scaling of noise (scaledNoise), generation of new initial conditions (genIC), parameters (genParams) and whether to integrate or not (integrate). The user modifiable simulation options can be specified as other arguments. This list should be used if one wants to modify many settings for multiple simulations.