sRACIPE is a systems biology tool to study the role of noise and parameter variation in gene regulatory circuits. It implements a randomization-based method for gene circuit modeling. It allows us to study the effect of both the gene expression noise and the parametric variation on any gene regulatory circuit (GRC) using only its topology, and simulates an ensemble of models with random kinetic parameters at multiple noise levels. Statistical analysis of the generated gene expressions reveals the basin of attraction and stability of various phenotypic states and their changes associated with intrinsic and extrinsic noises. sRACIPE provides a holistic picture to evaluate the effects of both the stochastic nature of cellular processes and the parametric variation.
sracipeSimulate
Primary function to simulate a circuit.
Contains options for plotting as well.
sracipeKnockDown
In-silico knockdown analysis of the circuit. Plots the relative changes in
different cluster proportions.
sracipeOverExp
In-silico over expression analysis of the circuit.
Plots the relative changes in
different cluster proportions.
sracipePlotData
Plot the simulated data. Includes options to plot the hierarchichal
clustering analysis, principal components, and uniform manifold
approximation and projection. Can plot the stochastic as well as the
knockout simulations.
sracipeSimulate, sracipeKnockDown,
sracipeOverExp, sracipePlotData