Gene Circuit Explorer (GeneEx) is a systems-biology tool to visualize and simulate gene regulatory circuits (GRCs). It can simulate a single model with specific kinetic parameters or an ensemble of models using the random circuit perturbation approach with and without stochastic effects (sRACIPE/RACIPE) for a comprehensive understanding of the structure and function of the GRCs in cell populations. The randomization-based methods (RACIPE/sRACIPE) enable study of the effects of both the gene expression noise and the parametric variation on any GRC using only its topology by simulating an ensemble of models with random kinetic parameters at multiple noise levels. Statistical analysis of the generated gene expressions reveal the basin of attraction and stability of various phenotypic states generated by the GRC. Thus, GeneEx provides a holistic picture to evaluate the effects of both the stochastic nature of cellular processes and the parametric variation on GRCs.
GeneEx is based on sRACIPE R package available from BioConductor. Additional tutorials on sRACIPE and GeneEx are available here.
If you use this website in your reserach, please cite the papers Interrogating the topological robustness of gene regulatory circuits by randomization published in PLoS computational biology 13 (3), e1005456 and Role of noise and parametric variation in the dynamics of gene regulatory circuits published in npj Systems Biology and Applications, 4, 40 (2018).