Fig. 1
From: RACIPE: a computational tool for modeling gene regulatory circuits using randomization
The computational tool of random circuit perturbation (a) Workflow of RACIPE. The only input for the tool is the circuit topology information. RACIPE automatically estimates the ranges of kinetic parameters for randomization and, from these ranges, randomly samples a particular set of parameters for a model. Then, it simulates the rate equations for this model to find all possible stable states. This procedure is repeated for many times to generate an ensemble of models. Finally, the tool outputs, from all the models, the kinetic parameters and the simulated gene expression of all stable states. b RACIPE is tested on two types of coupled toggle-switch (CTS) circuits (diagram illustrated in the top panel). The arrows represent transcriptional activation; the bar-headed arrows represent transcriptional inhibition. For both of the cases, the average time cost to simulate a RACIPE model (y-axis) is linearly proportional to the number of model parameters (x-axis)